HEADER TRANSFERASE 15-DEC-10 2Y2L TITLE PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL TITLE 2 BORONATE (E06) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 1B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: TRANSPEPTIDASE DOMAIN, RESIDUES 101-125,323-791; COMPND 5 SYNONYM: PBP1B; COMPND 6 EC: 2.4.1.129, 2.3.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: ALKYL BORONATE (E06) COVALENTLY BOND TO S460 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 171101; SOURCE 4 STRAIN: R6; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX KEYWDS TRANSFERASE, INFECTION, CELL WALL, PEPTIDOGLYCAN, INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR C.CONTRERAS-MARTEL,A.AMOROSO,E.C.WOON,A.ZERVOSEN,S.INGLIS,A.MARTINS, AUTHOR 2 O.VERLAINE,A.RYDZIK,V.JOB,A.LUXEN,B.JORIS,C.J.SCHOFIELD,A.DESSEN REVDAT 4 20-DEC-23 2Y2L 1 REMARK LINK REVDAT 3 25-JAN-17 2Y2L 1 ATOM ANISOU REVDAT 2 28-SEP-11 2Y2L 1 JRNL REVDAT 1 03-AUG-11 2Y2L 0 JRNL AUTH C.CONTRERAS-MARTEL,A.AMOROSO,E.C.WOON,A.ZERVOSEN,S.INGLIS, JRNL AUTH 2 A.MARTINS,O.VERLAINE,A.RYDZIK,V.JOB,A.LUXEN,B.JORIS, JRNL AUTH 3 C.J.SCHOFIELD,A.DESSEN JRNL TITL STRUCTURE-GUIDED DESIGN OF CELL WALL BIOSYNTHESIS INHIBITORS JRNL TITL 2 THAT OVERCOME BETA-LACTAM RESISTANCE IN STAPHYLOCOCCUS JRNL TITL 3 AUREUS (MRSA). JRNL REF ACS CHEM.BIOL. V. 6 943 2011 JRNL REFN ISSN 1554-8929 JRNL PMID 21732689 JRNL DOI 10.1021/CB2001846 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0095 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 75250 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8403 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4322 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.4410 REMARK 3 BIN FREE R VALUE SET COUNT : 445 REMARK 3 BIN FREE R VALUE : 0.4730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7312 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 498 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.26000 REMARK 3 B22 (A**2) : 0.62000 REMARK 3 B33 (A**2) : 0.64000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.175 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.017 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7499 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10149 ; 1.471 ; 1.931 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 945 ; 7.702 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1115 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5608 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 5 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 107 A 125 5 REMARK 3 1 B 107 B 125 5 REMARK 3 2 A 335 A 789 5 REMARK 3 2 B 335 B 789 5 REMARK 3 3 A 1000 A 1000 4 REMARK 3 3 B 1000 B 1000 4 REMARK 3 4 A 1100 A 1300 6 REMARK 3 4 B 1100 B 1300 6 REMARK 3 5 A 1790 A 1790 6 REMARK 3 5 B 1790 B 1790 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1891 ; 0.21 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 1891 ; 0.21 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 1758 ; 0.46 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 1758 ; 0.46 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1891 ; 3.55 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 1891 ; 3.55 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 1758 ; 4.54 ; 10.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 1758 ; 4.54 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 6 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 104 A 125 REMARK 3 RESIDUE RANGE : B 104 B 125 REMARK 3 RESIDUE RANGE : A 337 A 393 REMARK 3 RESIDUE RANGE : B 337 B 393 REMARK 3 RESIDUE RANGE : A 585 A 601 REMARK 3 RESIDUE RANGE : B 585 B 601 REMARK 3 ORIGIN FOR THE GROUP (A): 72.8016 70.0980 35.7388 REMARK 3 T TENSOR REMARK 3 T11: 0.1015 T22: 0.2452 REMARK 3 T33: 0.0238 T12: -0.0723 REMARK 3 T13: 0.0173 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 3.4395 L22: 4.4716 REMARK 3 L33: 0.3757 L12: -3.4479 REMARK 3 L13: 0.1767 L23: -0.2153 REMARK 3 S TENSOR REMARK 3 S11: 0.0234 S12: 0.2487 S13: -0.0046 REMARK 3 S21: -0.1553 S22: -0.0542 S23: -0.1193 REMARK 3 S31: 0.0245 S32: 0.0658 S33: 0.0308 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 394 A 584 REMARK 3 RESIDUE RANGE : B 394 B 584 REMARK 3 RESIDUE RANGE : A 602 A 722 REMARK 3 RESIDUE RANGE : B 602 B 722 REMARK 3 ORIGIN FOR THE GROUP (A): 72.4421 73.6853 54.3959 REMARK 3 T TENSOR REMARK 3 T11: 0.0199 T22: 0.0203 REMARK 3 T33: 0.0122 T12: -0.0128 REMARK 3 T13: 0.0115 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.9428 L22: 1.1774 REMARK 3 L33: 0.4049 L12: -0.7191 REMARK 3 L13: 0.0288 L23: -0.1473 REMARK 3 S TENSOR REMARK 3 S11: -0.0077 S12: 0.0648 S13: 0.0543 REMARK 3 S21: 0.0351 S22: -0.0041 S23: -0.0494 REMARK 3 S31: -0.0185 S32: -0.0230 S33: 0.0118 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 723 A 790 REMARK 3 RESIDUE RANGE : B 723 B 790 REMARK 3 ORIGIN FOR THE GROUP (A): 72.4429 77.7470 80.2947 REMARK 3 T TENSOR REMARK 3 T11: 0.4004 T22: 0.4808 REMARK 3 T33: 0.2000 T12: -0.0882 REMARK 3 T13: 0.0206 T23: -0.1376 REMARK 3 L TENSOR REMARK 3 L11: 0.6806 L22: 2.3872 REMARK 3 L33: 1.4654 L12: -1.1671 REMARK 3 L13: 0.2712 L23: -0.1984 REMARK 3 S TENSOR REMARK 3 S11: -0.3794 S12: -0.2587 S13: 0.1423 REMARK 3 S21: 0.9248 S22: 0.1190 S23: -0.0857 REMARK 3 S31: -0.1196 S32: -0.0726 S33: 0.2604 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U REMARK 3 VALUES WITH TLS ADDED REMARK 4 REMARK 4 2Y2L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1290046722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93340 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85632 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 44.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 35.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48000 REMARK 200 FOR SHELL : 3.090 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2BG1 REMARK 200 REMARK 200 REMARK: MOLECULAR REPLACEMENT MODEL 2BG1 WITHOUT RESIDUES 654 TO REMARK 200 660 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM HEPES PH 7.2, 3M NACL, 0.6-0.9M REMARK 280 AMMONIUM SULFATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 48.02750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.77850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.81400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.77850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.02750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.81400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -367.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 656 TO GLY REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ARG 687 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASN 656 TO GLY REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ARG 686 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ARG 687 TO GLN REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 101 REMARK 465 ILE A 102 REMARK 465 SER A 103 REMARK 465 SER A 104 REMARK 465 ASP A 122 REMARK 465 LEU A 123 REMARK 465 LEU A 124 REMARK 465 ARG A 125 REMARK 465 GLN A 323 REMARK 465 ASP A 324 REMARK 465 PHE A 325 REMARK 465 LEU A 326 REMARK 465 PRO A 327 REMARK 465 SER A 328 REMARK 465 GLY A 329 REMARK 465 THR A 330 REMARK 465 VAL A 331 REMARK 465 THR A 332 REMARK 465 GLY A 333 REMARK 465 ILE A 334 REMARK 465 SER A 335 REMARK 465 PRO A 791 REMARK 465 ASP B 101 REMARK 465 ILE B 102 REMARK 465 SER B 103 REMARK 465 SER B 104 REMARK 465 ARG B 125 REMARK 465 GLN B 323 REMARK 465 ASP B 324 REMARK 465 PHE B 325 REMARK 465 LEU B 326 REMARK 465 PRO B 327 REMARK 465 SER B 328 REMARK 465 GLY B 329 REMARK 465 THR B 330 REMARK 465 VAL B 331 REMARK 465 THR B 332 REMARK 465 GLY B 333 REMARK 465 ILE B 137 REMARK 465 PRO B 791 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O SER B 789 CA LEU B 790 0.42 REMARK 500 O SER B 789 N LEU B 790 1.07 REMARK 500 C SER B 789 CA LEU B 790 1.52 REMARK 500 CA SER B 789 N LEU B 790 1.57 REMARK 500 O SER B 789 CB LEU B 790 1.74 REMARK 500 NZ LYS B 381 O HOH B 2011 1.78 REMARK 500 O SER B 789 C LEU B 790 1.79 REMARK 500 O HOH B 2065 O HOH B 2158 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 789 C LEU A 790 N -0.151 REMARK 500 SER B 789 C LEU B 790 N -0.169 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 456 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 LEU B 483 CA - CB - CG ANGL. DEV. = 16.1 DEGREES REMARK 500 SER B 789 CA - C - N ANGL. DEV. = -47.6 DEGREES REMARK 500 SER B 789 O - C - N ANGL. DEV. = -69.5 DEGREES REMARK 500 LEU B 790 C - N - CA ANGL. DEV. = -52.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 415 -147.99 -137.58 REMARK 500 ASN A 442 94.49 179.54 REMARK 500 ALA A 459 -140.89 53.44 REMARK 500 ALA A 467 -74.97 -99.00 REMARK 500 ALA A 499 -123.87 57.09 REMARK 500 THR A 504 -97.83 -133.67 REMARK 500 MET A 507 143.32 -170.59 REMARK 500 ASN A 576 36.04 -77.06 REMARK 500 SER A 691 -61.06 -108.56 REMARK 500 SER A 708 80.91 -153.24 REMARK 500 VAL A 741 79.41 -114.40 REMARK 500 GLU A 742 87.24 55.76 REMARK 500 LYS A 744 119.38 -28.53 REMARK 500 ASN A 759 -166.73 -106.62 REMARK 500 LEU B 366 -5.61 -59.22 REMARK 500 ASN B 442 99.25 -179.93 REMARK 500 ALA B 459 -140.69 62.82 REMARK 500 THR B 461 1.27 -66.79 REMARK 500 ALA B 467 -79.15 -107.25 REMARK 500 ALA B 499 -113.23 39.30 REMARK 500 THR B 504 -106.18 -130.44 REMARK 500 ASN B 576 40.44 -81.33 REMARK 500 ASN B 640 86.28 -167.16 REMARK 500 SER B 708 85.33 -150.40 REMARK 500 GLU B 742 70.86 59.70 REMARK 500 LYS B 744 108.75 -50.66 REMARK 500 ASN B 759 -160.66 -103.72 REMARK 500 SER B 789 -43.60 -152.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 416 THR A 417 -143.61 REMARK 500 SER B 666 THR B 667 148.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER B 789 16.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 (R)-(1-(2,6-DIFLUOROBENZAMIDO)ETHYL)BORONIC ACID (E06): REMARK 600 COVALENTLY BOND TO SER 460 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1300 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 652 OG1 REMARK 620 2 THR A 654 OG1 133.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1300 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 652 OG1 REMARK 620 2 THR B 654 OG1 133.0 REMARK 620 3 E06 B1000 O2 124.2 102.4 REMARK 620 4 HOH B2082 O 110.8 79.0 82.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE E06 A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1214 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1215 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1218 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1220 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1229 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1300 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1791 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE E06 B 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1100 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1206 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1208 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1214 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1215 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1218 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1219 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1220 REMARK 800 REMARK 800 SITE_IDENTIFIER: EC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: EC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1300 REMARK 800 REMARK 800 SITE_IDENTIFIER: EC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1792 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2UWX RELATED DB: PDB REMARK 900 ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A REMARK 900 PENICILLIN-BINDING PROTEINS REMARK 900 RELATED ID: 2XD1 RELATED DB: PDB REMARK 900 ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A REMARK 900 PENICILLIN-BINDING PROTEINS REMARK 900 RELATED ID: 2XD5 RELATED DB: PDB REMARK 900 STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM AND THE ROLE OF REMARK 900 STREPTOCOCCUS PNEUMONIAE PBP1B REMARK 900 RELATED ID: 2Y2I RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (ZA3) REMARK 900 RELATED ID: 2Y2G RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (A01) REMARK 900 RELATED ID: 2Y2H RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (ZA2) REMARK 900 RELATED ID: 2Y2O RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (EO9) REMARK 900 RELATED ID: 2Y2N RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (E07) REMARK 900 RELATED ID: 2Y2J RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (ZA4) REMARK 900 RELATED ID: 2Y2K RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (ZA5) REMARK 900 RELATED ID: 2Y2M RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (E08) REMARK 900 RELATED ID: 2Y2Q RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (Z06) REMARK 900 RELATED ID: 2Y2P RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL REMARK 900 BORONATE (Z10) DBREF 2Y2L A 101 125 UNP Q7CRA4 Q7CRA4_STRR6 101 125 DBREF 2Y2L A 323 791 UNP Q7CRA4 Q7CRA4_STRR6 323 791 DBREF 2Y2L B 101 125 UNP Q7CRA4 Q7CRA4_STRR6 101 125 DBREF 2Y2L B 323 791 UNP Q7CRA4 Q7CRA4_STRR6 323 791 SEQADV 2Y2L GLY A 656 UNP Q7CRA4 ASN 656 ENGINEERED MUTATION SEQADV 2Y2L GLN A 686 UNP Q7CRA4 ARG 686 ENGINEERED MUTATION SEQADV 2Y2L GLN A 687 UNP Q7CRA4 ARG 687 ENGINEERED MUTATION SEQADV 2Y2L GLY B 656 UNP Q7CRA4 ASN 656 ENGINEERED MUTATION SEQADV 2Y2L GLN B 686 UNP Q7CRA4 ARG 686 ENGINEERED MUTATION SEQADV 2Y2L GLN B 687 UNP Q7CRA4 ARG 687 ENGINEERED MUTATION SEQRES 1 A 494 ASP ILE SER SER ILE SER GLU ILE THR TYR SER ASP GLY SEQRES 2 A 494 THR VAL ILE ALA SER ILE GLU SER ASP LEU LEU ARG GLN SEQRES 3 A 494 ASP PHE LEU PRO SER GLY THR VAL THR GLY ILE SER ARG SEQRES 4 A 494 ASP TYR LEU TYR PHE THR THR LEU ALA GLU ALA GLN GLU SEQRES 5 A 494 ARG MET TYR ASP TYR LEU ALA GLN ARG ASP ASN VAL SER SEQRES 6 A 494 ALA LYS GLU LEU LYS ASN GLU ALA THR GLN LYS PHE TYR SEQRES 7 A 494 ARG ASP LEU ALA ALA LYS GLU ILE GLU ASN GLY GLY TYR SEQRES 8 A 494 LYS ILE THR THR THR ILE ASP GLN LYS ILE HIS SER ALA SEQRES 9 A 494 MET GLN SER ALA VAL ALA ASP TYR GLY TYR LEU LEU ASP SEQRES 10 A 494 ASP GLY THR GLY ARG VAL GLU VAL GLY ASN VAL LEU MET SEQRES 11 A 494 ASP ASN GLN THR GLY ALA ILE LEU GLY PHE VAL GLY GLY SEQRES 12 A 494 ARG ASN TYR GLN GLU ASN GLN ASN ASN HIS ALA PHE ASP SEQRES 13 A 494 THR LYS ARG SER PRO ALA SER THR THR LYS PRO LEU LEU SEQRES 14 A 494 ALA TYR GLY ILE ALA ILE ASP GLN GLY LEU MET GLY SER SEQRES 15 A 494 GLU THR ILE LEU SER ASN TYR PRO THR ASN PHE ALA ASN SEQRES 16 A 494 GLY ASN PRO ILE MET TYR ALA ASN SER LYS GLY THR GLY SEQRES 17 A 494 MET MET THR LEU GLY GLU ALA LEU ASN TYR SER TRP ASN SEQRES 18 A 494 ILE PRO ALA TYR TRP THR TYR ARG MET LEU ARG GLU ASN SEQRES 19 A 494 GLY VAL ASP VAL LYS GLY TYR MET GLU LYS MET GLY TYR SEQRES 20 A 494 GLU ILE PRO GLU TYR GLY ILE GLU SER LEU PRO MET GLY SEQRES 21 A 494 GLY GLY ILE GLU VAL THR VAL ALA GLN HIS THR ASN GLY SEQRES 22 A 494 TYR GLN THR LEU ALA ASN ASN GLY VAL TYR HIS GLN LYS SEQRES 23 A 494 HIS VAL ILE SER LYS ILE GLU ALA ALA ASP GLY ARG VAL SEQRES 24 A 494 VAL TYR GLU TYR GLN ASP LYS PRO VAL GLN VAL TYR SER SEQRES 25 A 494 LYS ALA THR ALA THR ILE MET GLN GLY LEU LEU ARG GLU SEQRES 26 A 494 VAL LEU SER SER ARG VAL THR THR THR PHE LYS SER ASN SEQRES 27 A 494 LEU THR SER LEU ASN PRO THR LEU ALA ASN ALA ASP TRP SEQRES 28 A 494 ILE GLY LYS THR GLY THR THR GLY GLN ASP GLU ASN MET SEQRES 29 A 494 TRP LEU MET LEU SER THR PRO ARG LEU THR LEU GLY GLY SEQRES 30 A 494 TRP ILE GLY HIS ASP ASP ASN HIS SER LEU SER GLN GLN SEQRES 31 A 494 ALA GLY TYR SER ASN ASN SER ASN TYR MET ALA HIS LEU SEQRES 32 A 494 VAL ASN ALA ILE GLN GLN ALA SER PRO SER ILE TRP GLY SEQRES 33 A 494 ASN GLU ARG PHE ALA LEU ASP PRO SER VAL VAL LYS SER SEQRES 34 A 494 GLU VAL LEU LYS SER THR GLY GLN LYS PRO GLY LYS VAL SEQRES 35 A 494 SER VAL GLU GLY LYS GLU VAL GLU VAL THR GLY SER THR SEQRES 36 A 494 VAL THR SER TYR TRP ALA ASN LYS SER GLY ALA PRO ALA SEQRES 37 A 494 THR SER TYR ARG PHE ALA ILE GLY GLY SER ASP ALA ASP SEQRES 38 A 494 TYR GLN ASN ALA TRP SER SER ILE VAL GLY SER LEU PRO SEQRES 1 B 494 ASP ILE SER SER ILE SER GLU ILE THR TYR SER ASP GLY SEQRES 2 B 494 THR VAL ILE ALA SER ILE GLU SER ASP LEU LEU ARG GLN SEQRES 3 B 494 ASP PHE LEU PRO SER GLY THR VAL THR GLY ILE SER ARG SEQRES 4 B 494 ASP TYR LEU TYR PHE THR THR LEU ALA GLU ALA GLN GLU SEQRES 5 B 494 ARG MET TYR ASP TYR LEU ALA GLN ARG ASP ASN VAL SER SEQRES 6 B 494 ALA LYS GLU LEU LYS ASN GLU ALA THR GLN LYS PHE TYR SEQRES 7 B 494 ARG ASP LEU ALA ALA LYS GLU ILE GLU ASN GLY GLY TYR SEQRES 8 B 494 LYS ILE THR THR THR ILE ASP GLN LYS ILE HIS SER ALA SEQRES 9 B 494 MET GLN SER ALA VAL ALA ASP TYR GLY TYR LEU LEU ASP SEQRES 10 B 494 ASP GLY THR GLY ARG VAL GLU VAL GLY ASN VAL LEU MET SEQRES 11 B 494 ASP ASN GLN THR GLY ALA ILE LEU GLY PHE VAL GLY GLY SEQRES 12 B 494 ARG ASN TYR GLN GLU ASN GLN ASN ASN HIS ALA PHE ASP SEQRES 13 B 494 THR LYS ARG SER PRO ALA SER THR THR LYS PRO LEU LEU SEQRES 14 B 494 ALA TYR GLY ILE ALA ILE ASP GLN GLY LEU MET GLY SER SEQRES 15 B 494 GLU THR ILE LEU SER ASN TYR PRO THR ASN PHE ALA ASN SEQRES 16 B 494 GLY ASN PRO ILE MET TYR ALA ASN SER LYS GLY THR GLY SEQRES 17 B 494 MET MET THR LEU GLY GLU ALA LEU ASN TYR SER TRP ASN SEQRES 18 B 494 ILE PRO ALA TYR TRP THR TYR ARG MET LEU ARG GLU ASN SEQRES 19 B 494 GLY VAL ASP VAL LYS GLY TYR MET GLU LYS MET GLY TYR SEQRES 20 B 494 GLU ILE PRO GLU TYR GLY ILE GLU SER LEU PRO MET GLY SEQRES 21 B 494 GLY GLY ILE GLU VAL THR VAL ALA GLN HIS THR ASN GLY SEQRES 22 B 494 TYR GLN THR LEU ALA ASN ASN GLY VAL TYR HIS GLN LYS SEQRES 23 B 494 HIS VAL ILE SER LYS ILE GLU ALA ALA ASP GLY ARG VAL SEQRES 24 B 494 VAL TYR GLU TYR GLN ASP LYS PRO VAL GLN VAL TYR SER SEQRES 25 B 494 LYS ALA THR ALA THR ILE MET GLN GLY LEU LEU ARG GLU SEQRES 26 B 494 VAL LEU SER SER ARG VAL THR THR THR PHE LYS SER ASN SEQRES 27 B 494 LEU THR SER LEU ASN PRO THR LEU ALA ASN ALA ASP TRP SEQRES 28 B 494 ILE GLY LYS THR GLY THR THR GLY GLN ASP GLU ASN MET SEQRES 29 B 494 TRP LEU MET LEU SER THR PRO ARG LEU THR LEU GLY GLY SEQRES 30 B 494 TRP ILE GLY HIS ASP ASP ASN HIS SER LEU SER GLN GLN SEQRES 31 B 494 ALA GLY TYR SER ASN ASN SER ASN TYR MET ALA HIS LEU SEQRES 32 B 494 VAL ASN ALA ILE GLN GLN ALA SER PRO SER ILE TRP GLY SEQRES 33 B 494 ASN GLU ARG PHE ALA LEU ASP PRO SER VAL VAL LYS SER SEQRES 34 B 494 GLU VAL LEU LYS SER THR GLY GLN LYS PRO GLY LYS VAL SEQRES 35 B 494 SER VAL GLU GLY LYS GLU VAL GLU VAL THR GLY SER THR SEQRES 36 B 494 VAL THR SER TYR TRP ALA ASN LYS SER GLY ALA PRO ALA SEQRES 37 B 494 THR SER TYR ARG PHE ALA ILE GLY GLY SER ASP ALA ASP SEQRES 38 B 494 TYR GLN ASN ALA TRP SER SER ILE VAL GLY SER LEU PRO HET E06 A1000 16 HET SO4 A1100 5 HET CL A1200 1 HET CL A1201 1 HET CL A1202 1 HET CL A1208 1 HET CL A1211 1 HET CL A1212 1 HET CL A1213 1 HET CL A1214 1 HET CL A1215 1 HET CL A1216 1 HET CL A1217 1 HET CL A1218 1 HET CL A1220 1 HET CL A1221 1 HET CL A1229 1 HET NA A1300 1 HET CL A1791 1 HET E06 B1000 16 HET SO4 B1100 5 HET CL B1200 1 HET CL B1201 1 HET CL B1202 1 HET CL B1206 1 HET CL B1208 1 HET CL B1211 1 HET CL B1212 1 HET CL B1213 1 HET CL B1214 1 HET CL B1215 1 HET CL B1216 1 HET CL B1217 1 HET CL B1218 1 HET CL B1219 1 HET CL B1220 1 HET CL B1221 1 HET NA B1300 1 HET CL B1792 1 HETNAM E06 [(1R)-1-[(2,6-DIFLUOROPHENYL)CARBONYLAMINO]ETHYL]- HETNAM 2 E06 TRIHYDROXY-BORON HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 3 E06 2(C9 H11 B F2 N O4 1-) FORMUL 4 SO4 2(O4 S 2-) FORMUL 5 CL 33(CL 1-) FORMUL 20 NA 2(NA 1+) FORMUL 42 HOH *498(H2 O) HELIX 1 1 ASP A 337 ASP A 359 1 23 HELIX 2 2 SER A 362 LYS A 367 1 6 HELIX 3 3 ASN A 368 GLY A 386 1 19 HELIX 4 4 ASP A 395 GLY A 410 1 16 HELIX 5 5 TYR A 411 ASP A 414 5 4 HELIX 6 6 PRO A 458 SER A 460 5 3 HELIX 7 7 THR A 461 ALA A 467 1 7 HELIX 8 8 ALA A 467 GLN A 474 1 8 HELIX 9 9 LEU A 509 SER A 516 1 8 HELIX 10 10 ASN A 518 ASN A 531 1 14 HELIX 11 11 ASP A 534 LYS A 541 1 8 HELIX 12 12 SER A 553 GLY A 557 5 5 HELIX 13 13 THR A 563 ASN A 576 1 14 HELIX 14 14 SER A 609 SER A 626 1 18 HELIX 15 15 THR A 631 ASN A 640 1 10 HELIX 16 16 ASN A 640 ASN A 645 1 6 HELIX 17 17 SER A 691 SER A 708 1 18 HELIX 18 18 SER A 775 SER A 789 1 15 HELIX 19 19 ASP B 337 ASP B 359 1 23 HELIX 20 20 ASN B 368 GLY B 386 1 19 HELIX 21 21 ASP B 395 GLY B 410 1 16 HELIX 22 22 TYR B 411 ASP B 414 5 4 HELIX 23 23 PRO B 458 THR B 461 5 4 HELIX 24 24 THR B 462 ALA B 467 1 6 HELIX 25 25 ALA B 467 GLN B 474 1 8 HELIX 26 26 LEU B 509 SER B 516 1 8 HELIX 27 27 ASN B 518 ASN B 531 1 14 HELIX 28 28 ASP B 534 MET B 542 1 9 HELIX 29 29 SER B 553 GLY B 557 5 5 HELIX 30 30 THR B 563 ASN B 576 1 14 HELIX 31 31 SER B 609 ARG B 627 1 19 HELIX 32 32 THR B 631 ASN B 640 1 10 HELIX 33 33 ASN B 640 ASN B 645 1 6 HELIX 34 34 SER B 691 SER B 708 1 18 HELIX 35 35 SER B 775 GLY B 788 1 14 SHEET 1 AA 5 VAL A 115 ILE A 119 0 SHEET 2 AA 5 SER A 106 THR A 109 -1 O SER A 106 N ILE A 119 SHEET 3 AA 5 LYS A 389 THR A 392 1 O ILE A 390 N THR A 109 SHEET 4 AA 5 ILE A 586 GLU A 590 -1 N SER A 587 O THR A 391 SHEET 5 AA 5 VAL A 596 GLU A 599 -1 N VAL A 597 O ILE A 589 SHEET 1 AB 5 ILE A 434 VAL A 438 0 SHEET 2 AB 5 GLU A 421 ASP A 428 -1 O ASN A 424 N VAL A 438 SHEET 3 AB 5 LEU A 670 GLY A 677 -1 O THR A 671 N MET A 427 SHEET 4 AB 5 ASN A 660 SER A 666 -1 O MET A 661 N ILE A 676 SHEET 5 AB 5 ILE A 649 THR A 654 -1 O ILE A 649 N SER A 666 SHEET 1 AC 2 ILE A 482 SER A 484 0 SHEET 2 AC 2 MET A 506 THR A 508 -1 O MET A 507 N LEU A 483 SHEET 1 AD 2 VAL A 579 TYR A 580 0 SHEET 2 AD 2 VAL A 605 GLN A 606 -1 O VAL A 605 N TYR A 580 SHEET 1 AE 2 VAL A 724 LEU A 729 0 SHEET 2 AE 2 THR A 752 TRP A 757 -1 O VAL A 753 N VAL A 728 SHEET 1 AF 2 LYS A 738 SER A 740 0 SHEET 2 AF 2 GLU A 745 GLU A 747 -1 O VAL A 746 N VAL A 739 SHEET 1 BA 5 VAL B 115 ILE B 119 0 SHEET 2 BA 5 SER B 106 THR B 109 -1 O SER B 106 N ILE B 119 SHEET 3 BA 5 LYS B 389 THR B 392 1 O ILE B 390 N THR B 109 SHEET 4 BA 5 ILE B 586 GLU B 590 -1 N SER B 587 O THR B 391 SHEET 5 BA 5 VAL B 596 GLU B 599 -1 N VAL B 597 O ILE B 589 SHEET 1 BB 5 ILE B 434 VAL B 438 0 SHEET 2 BB 5 GLU B 421 ASP B 428 -1 O ASN B 424 N VAL B 438 SHEET 3 BB 5 LEU B 670 GLY B 677 -1 O THR B 671 N MET B 427 SHEET 4 BB 5 ASN B 660 SER B 666 -1 O MET B 661 N ILE B 676 SHEET 5 BB 5 ILE B 649 THR B 654 -1 O ILE B 649 N SER B 666 SHEET 1 BC 2 ILE B 482 SER B 484 0 SHEET 2 BC 2 MET B 506 THR B 508 -1 O MET B 507 N LEU B 483 SHEET 1 BD 2 VAL B 579 TYR B 580 0 SHEET 2 BD 2 VAL B 605 GLN B 606 -1 O VAL B 605 N TYR B 580 SHEET 1 BE 2 VAL B 724 LEU B 729 0 SHEET 2 BE 2 THR B 752 TRP B 757 -1 O VAL B 753 N VAL B 728 SHEET 1 BF 2 GLY B 737 VAL B 741 0 SHEET 2 BF 2 LYS B 744 VAL B 748 -1 O LYS B 744 N VAL B 741 LINK OG SER A 460 B E06 A1000 1555 1555 1.54 LINK OG SER B 460 B E06 B1000 1555 1555 1.54 LINK OG1 THR A 652 NA NA A1300 1555 1555 3.04 LINK OG1 THR A 654 NA NA A1300 1555 1555 3.05 LINK OG1 THR B 652 NA NA B1300 1555 1555 3.13 LINK OG1 THR B 654 NA NA B1300 1555 1555 3.07 LINK O2 E06 B1000 NA NA B1300 1555 1555 3.17 LINK NA NA B1300 O HOH B2082 1555 1555 2.99 SITE 1 AC1 13 ALA A 459 SER A 460 TYR A 498 SER A 516 SITE 2 AC1 13 ASN A 518 MET A 556 GLY A 557 GLY A 558 SITE 3 AC1 13 THR A 654 THR A 655 NA A1300 HOH A2081 SITE 4 AC1 13 ASN B 492 SITE 1 AC2 7 THR A 563 GLN A 566 LYS A 583 HOH A2114 SITE 2 AC2 7 HOH A2247 HOH A2248 HOH A2249 SITE 1 AC3 3 ARG A 529 HOH A2122 ARG B 529 SITE 1 AC4 3 VAL A 535 LYS A 536 HOH A2102 SITE 1 AC5 2 ARG A 627 LYS A 633 SITE 1 AC6 2 GLU A 727 LYS A 735 SITE 1 AC7 3 GLU A 545 VAL A 562 HOH A2114 SITE 1 AC8 3 VAL A 585 ILE A 586 HOH A2007 SITE 1 AC9 5 ASP A 337 TYR A 338 LEU A 339 HIS A 399 SITE 2 AC9 5 GLN A 403 SITE 1 BC1 1 LYS A 610 SITE 1 BC2 2 HIS A 699 ASN A 702 SITE 1 BC3 3 TYR A 110 ASP A 112 GLN A 396 SITE 1 BC4 2 LYS A 760 SER A 761 SITE 1 BC5 3 SER A 775 ASP A 776 ALA A 777 SITE 1 BC6 2 ALA A 718 LEU A 719 SITE 1 BC7 3 TYR A 768 ASP A 776 GLN A 780 SITE 1 BC8 3 ASP A 679 ASP A 680 HOH A2190 SITE 1 BC9 4 THR A 652 GLY A 653 THR A 654 E06 A1000 SITE 1 CC1 2 SER A 634 SER B 634 SITE 1 CC2 13 ALA A 491 ALA B 459 SER B 460 LYS B 463 SITE 2 CC2 13 SER B 516 ASN B 518 MET B 556 GLY B 557 SITE 3 CC2 13 GLY B 558 THR B 654 THR B 655 NA B1300 SITE 4 CC2 13 HOH B2074 SITE 1 CC3 8 THR B 563 GLN B 566 LYS B 583 HOH B2116 SITE 2 CC3 8 HOH B2129 HOH B2247 HOH B2248 HOH B2249 SITE 1 CC4 2 ARG A 529 ARG B 529 SITE 1 CC5 3 VAL B 535 LYS B 536 HOH B2103 SITE 1 CC6 3 SER B 625 ARG B 627 LYS B 633 SITE 1 CC7 2 ASP B 593 HOH B2035 SITE 1 CC8 2 GLU B 727 LYS B 735 SITE 1 CC9 5 TYR B 544 GLU B 545 HOH B2051 HOH B2116 SITE 2 CC9 5 HOH B2247 SITE 1 DC1 4 GLU B 346 VAL B 585 ILE B 586 HOH B2005 SITE 1 DC2 4 ASP B 337 TYR B 338 LEU B 339 HIS B 399 SITE 1 DC3 1 LYS B 610 SITE 1 DC4 2 HIS B 699 ASN B 702 SITE 1 DC5 4 TYR B 110 SER B 111 ASP B 112 GLN B 396 SITE 1 DC6 3 ASN B 759 LYS B 760 SER B 761 SITE 1 DC7 2 SER B 775 ALA B 777 SITE 1 DC8 1 LYS B 725 SITE 1 DC9 2 ALA B 718 LEU B 719 SITE 1 EC1 3 TYR B 768 ASP B 776 GLN B 780 SITE 1 EC2 5 THR B 652 GLY B 653 THR B 654 E06 B1000 SITE 2 EC2 5 HOH B2082 SITE 1 EC3 4 ASN A 492 ASN A 494 ASN B 492 ASN B 494 CRYST1 96.055 101.628 145.557 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010411 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009840 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006870 0.00000 MTRIX1 1 -0.999413 0.032825 -0.009768 143.42473 1 MTRIX2 1 -0.034248 -0.957122 0.287655 131.29225 1 MTRIX3 1 0.000093 0.287820 0.957684 -18.92054 1