HEADER ANTIBIOTIC 20-JUL-17 5OJ1 TITLE PENICILLIN BINDING PROTEIN 2X (PBP2X) FROM S.PNEUMONIAE IN COMPLEX TITLE 2 WITH OXACILLIN AND A TETRASACCHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 2X; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PBP2X; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE R6; SOURCE 3 ORGANISM_TAXID: 171101; SOURCE 4 GENE: PBPX, SPR0304; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PENICILLIN-BINDING-PROTEIN, CELL-WALL, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR N.BERNARDO-GARCIA,J.A.HERMOSO REVDAT 2 17-JAN-24 5OJ1 1 COMPND HETNAM REVDAT 1 30-MAY-18 5OJ1 0 JRNL AUTH N.BERNARDO-GARCIA,K.V.MAHASENAN,M.T.BATUECAS,M.LEE,D.HESEK, JRNL AUTH 2 D.PETRACKOVA,L.DOUBRAVOVA,P.BRANNY,S.MOBASHERY,J.A.HERMOSO JRNL TITL ALLOSTERY, RECOGNITION OF NASCENT PEPTIDOGLYCAN, AND JRNL TITL 2 CROSS-LINKING OF THE CELL WALL BY THE ESSENTIAL JRNL TITL 3 PENICILLIN-BINDING PROTEIN 2X OF STREPTOCOCCUS PNEUMONIAE. JRNL REF ACS CHEM. BIOL. V. 13 694 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 29357220 JRNL DOI 10.1021/ACSCHEMBIO.7B00817 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25437 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1303 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) : 2.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1857 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.1300 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.2060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5178 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.532 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.302 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.171 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.155 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5322 ; 0.014 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4856 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7218 ; 1.761 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11338 ; 1.069 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 677 ; 8.259 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 233 ;41.736 ;25.880 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 917 ;18.404 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.256 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 818 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5956 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 992 ; 0.002 ; 0.020 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): 2708 ; 5.146 ; 7.115 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2707 ; 5.144 ; 7.114 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3385 ; 7.621 ;10.667 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3386 ; 7.620 ;10.668 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2614 ; 5.309 ; 7.465 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2612 ; 5.292 ; 7.462 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3833 ; 7.606 ;11.064 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5880 ;10.595 ;84.137 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5881 ;10.596 ;84.152 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 5OJ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97497 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26783 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 48.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.19200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1K25 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.3-3M NACL, 0.1M NA ACETATE PH 4.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.11800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 126.23600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 126.23600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.11800 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 GLY A 49 REMARK 465 THR A 50 REMARK 465 GLY A 51 REMARK 465 THR A 52 REMARK 465 ARG A 53 REMARK 465 PHE A 54 REMARK 465 GLY A 55 REMARK 465 THR A 56 REMARK 465 ASP A 57 REMARK 465 LEU A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 REMARK 465 GLU A 61 REMARK 465 ALA A 62 REMARK 465 LYS A 63 REMARK 465 LYS A 64 REMARK 465 VAL A 65 REMARK 465 HIS A 66 REMARK 465 GLN A 67 REMARK 465 THR A 68 REMARK 465 THR A 69 REMARK 465 ARG A 70 REMARK 465 THR A 71 REMARK 465 GLU A 237 REMARK 465 LYS A 238 REMARK 465 ASP A 239 REMARK 465 ARG A 240 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 ASP A 409 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 485 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 512 NE - CZ - NH2 ANGL. DEV. = -3.1 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 ASN A 103 -101.01 61.72 REMARK 500 TYR A 104 49.43 -101.67 REMARK 500 LYS A 105 117.63 -173.79 REMARK 500 SER A 106 57.62 -176.18 REMARK 500 THR A 108 -35.11 69.36 REMARK 500 LYS A 147 -91.78 -144.16 REMARK 500 GLU A 169 -32.08 72.75 REMARK 500 GLU A 174 -78.48 64.13 REMARK 500 VAL A 175 18.05 29.38 REMARK 500 ASP A 179 -159.02 -117.66 REMARK 500 ASN A 243 -77.30 -85.48 REMARK 500 ILE A 244 149.56 -179.37 REMARK 500 GLN A 253 59.81 -166.48 REMARK 500 LYS A 285 72.09 59.31 REMARK 500 ALA A 303 132.70 -170.06 REMARK 500 ALA A 312 -55.85 75.77 REMARK 500 THR A 352 56.34 -116.78 REMARK 500 ASN A 360 173.69 -59.36 REMARK 500 SER A 362 -18.01 -39.75 REMARK 500 GLU A 363 -93.98 49.93 REMARK 500 LEU A 364 106.93 114.92 REMARK 500 ALA A 369 117.37 160.15 REMARK 500 ASN A 397 -71.89 87.92 REMARK 500 ASN A 470 50.00 -94.06 REMARK 500 GLN A 489 62.39 28.63 REMARK 500 LYS A 505 -60.67 130.47 REMARK 500 VAL A 523 -51.55 -147.81 REMARK 500 ASN A 529 159.22 68.96 REMARK 500 HIS A 530 -173.11 72.22 REMARK 500 SER A 531 -35.31 -37.28 REMARK 500 ASN A 558 31.93 -141.56 REMARK 500 ASP A 567 77.65 -68.14 REMARK 500 ASN A 580 89.96 -158.63 REMARK 500 LYS A 615 -39.45 -30.51 REMARK 500 LYS A 625 -77.70 -149.70 REMARK 500 GLN A 632 -39.24 -170.81 REMARK 500 GLN A 633 113.52 80.88 REMARK 500 SER A 640 136.69 73.61 REMARK 500 GLN A 659 76.39 -109.29 REMARK 500 LYS A 739 -63.75 -4.77 REMARK 500 ASP A 740 86.68 -152.84 REMARK 500 LYS A 742 -71.15 -67.77 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 GLN A 143 PRO A 144 149.68 REMARK 500 GLU A 363 LEU A 364 -146.46 REMARK 500 TYR A 528 ASN A 529 49.16 REMARK 500 THR A 532 GLY A 533 145.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 927 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A 928 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 929 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH A 930 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A 931 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH A 932 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH A 933 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH A 934 DISTANCE = 7.39 ANGSTROMS REMARK 525 HOH A 935 DISTANCE = 7.70 ANGSTROMS REMARK 525 HOH A 936 DISTANCE = 7.86 ANGSTROMS REMARK 525 HOH A 937 DISTANCE = 8.50 ANGSTROMS REMARK 525 HOH A 938 DISTANCE = 8.93 ANGSTROMS REMARK 525 HOH A 939 DISTANCE = 9.53 ANGSTROMS REMARK 525 HOH A 940 DISTANCE = 11.07 ANGSTROMS REMARK 525 HOH A 941 DISTANCE = 11.08 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1S6 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 802 DBREF 5OJ1 A 49 750 UNP P59676 PBPX_STRR6 49 750 SEQRES 1 A 702 GLY THR GLY THR ARG PHE GLY THR ASP LEU ALA LYS GLU SEQRES 2 A 702 ALA LYS LYS VAL HIS GLN THR THR ARG THR VAL PRO ALA SEQRES 3 A 702 LYS ARG GLY THR ILE TYR ASP ARG ASN GLY VAL PRO ILE SEQRES 4 A 702 ALA GLU ASP ALA THR SER TYR ASN VAL TYR ALA VAL ILE SEQRES 5 A 702 ASP GLU ASN TYR LYS SER ALA THR GLY LYS ILE LEU TYR SEQRES 6 A 702 VAL GLU LYS THR GLN PHE ASN LYS VAL ALA GLU VAL PHE SEQRES 7 A 702 HIS LYS TYR LEU ASP MET GLU GLU SER TYR VAL ARG GLU SEQRES 8 A 702 GLN LEU SER GLN PRO ASN LEU LYS GLN VAL SER PHE GLY SEQRES 9 A 702 ALA LYS GLY ASN GLY ILE THR TYR ALA ASN MET MET SER SEQRES 10 A 702 ILE LYS LYS GLU LEU GLU ALA ALA GLU VAL LYS GLY ILE SEQRES 11 A 702 ASP PHE THR THR SER PRO ASN ARG SER TYR PRO ASN GLY SEQRES 12 A 702 GLN PHE ALA SER SER PHE ILE GLY LEU ALA GLN LEU HIS SEQRES 13 A 702 GLU ASN GLU ASP GLY SER LYS SER LEU LEU GLY THR SER SEQRES 14 A 702 GLY MET GLU SER SER LEU ASN SER ILE LEU ALA GLY THR SEQRES 15 A 702 ASP GLY ILE ILE THR TYR GLU LYS ASP ARG LEU GLY ASN SEQRES 16 A 702 ILE VAL PRO GLY THR GLU GLN VAL SER GLN ARG THR MET SEQRES 17 A 702 ASP GLY LYS ASP VAL TYR THR THR ILE SER SER PRO LEU SEQRES 18 A 702 GLN SER PHE MET GLU THR GLN MET ASP ALA PHE GLN GLU SEQRES 19 A 702 LYS VAL LYS GLY LYS TYR MET THR ALA THR LEU VAL SER SEQRES 20 A 702 ALA LYS THR GLY GLU ILE LEU ALA THR THR GLN ARG PRO SEQRES 21 A 702 THR PHE ASP ALA ASP THR LYS GLU GLY ILE THR GLU ASP SEQRES 22 A 702 PHE VAL TRP ARG ASP ILE LEU TYR GLN SER ASN TYR GLU SEQRES 23 A 702 PRO GLY SER THR MET LYS VAL MET MET LEU ALA ALA ALA SEQRES 24 A 702 ILE ASP ASN ASN THR PHE PRO GLY GLY GLU VAL PHE ASN SEQRES 25 A 702 SER SER GLU LEU LYS ILE ALA ASP ALA THR ILE ARG ASP SEQRES 26 A 702 TRP ASP VAL ASN GLU GLY LEU THR GLY GLY ARG MET MET SEQRES 27 A 702 THR PHE SER GLN GLY PHE ALA HIS SER SER ASN VAL GLY SEQRES 28 A 702 MET THR LEU LEU GLU GLN LYS MET GLY ASP ALA THR TRP SEQRES 29 A 702 LEU ASP TYR LEU ASN ARG PHE LYS PHE GLY VAL PRO THR SEQRES 30 A 702 ARG PHE GLY LEU THR ASP GLU TYR ALA GLY GLN LEU PRO SEQRES 31 A 702 ALA ASP ASN ILE VAL ASN ILE ALA GLN SER SER PHE GLY SEQRES 32 A 702 GLN GLY ILE SER VAL THR GLN THR GLN MET ILE ARG ALA SEQRES 33 A 702 PHE THR ALA ILE ALA ASN ASP GLY VAL MET LEU GLU PRO SEQRES 34 A 702 LYS PHE ILE SER ALA ILE TYR ASP PRO ASN ASP GLN THR SEQRES 35 A 702 ALA ARG LYS SER GLN LYS GLU ILE VAL GLY ASN PRO VAL SEQRES 36 A 702 SER LYS ASP ALA ALA SER LEU THR ARG THR ASN MET VAL SEQRES 37 A 702 LEU VAL GLY THR ASP PRO VAL TYR GLY THR MET TYR ASN SEQRES 38 A 702 HIS SER THR GLY LYS PRO THR VAL THR VAL PRO GLY GLN SEQRES 39 A 702 ASN VAL ALA LEU LYS SER GLY THR ALA GLN ILE ALA ASP SEQRES 40 A 702 GLU LYS ASN GLY GLY TYR LEU VAL GLY LEU THR ASP TYR SEQRES 41 A 702 ILE PHE SER ALA VAL SER MET SER PRO ALA GLU ASN PRO SEQRES 42 A 702 ASP PHE ILE LEU TYR VAL THR VAL GLN GLN PRO GLU HIS SEQRES 43 A 702 TYR SER GLY ILE GLN LEU GLY GLU PHE ALA ASN PRO ILE SEQRES 44 A 702 LEU GLU ARG ALA SER ALA MET LYS ASP SER LEU ASN LEU SEQRES 45 A 702 GLN THR THR ALA LYS ALA LEU GLU GLN VAL SER GLN GLN SEQRES 46 A 702 SER PRO TYR PRO MET PRO SER VAL LYS ASP ILE SER PRO SEQRES 47 A 702 GLY ASP LEU ALA GLU GLU LEU ARG ARG ASN LEU VAL GLN SEQRES 48 A 702 PRO ILE VAL VAL GLY THR GLY THR LYS ILE LYS ASN SER SEQRES 49 A 702 SER ALA GLU GLU GLY LYS ASN LEU ALA PRO ASN GLN GLN SEQRES 50 A 702 VAL LEU ILE LEU SER ASP LYS ALA GLU GLU VAL PRO ASP SEQRES 51 A 702 MET TYR GLY TRP THR LYS GLU THR ALA GLU THR LEU ALA SEQRES 52 A 702 LYS TRP LEU ASN ILE GLU LEU GLU PHE GLN GLY SER GLY SEQRES 53 A 702 SER THR VAL GLN LYS GLN ASP VAL ARG ALA ASN THR ALA SEQRES 54 A 702 ILE LYS ASP ILE LYS LYS ILE THR LEU THR LEU GLY ASP HET 1S6 A 801 28 HET NA A 802 1 HETNAM 1S6 (2R,4S)-5,5-DIMETHYL-2-[(1R)-1-{[(5-METHYL-3-PHENYL-1, HETNAM 2 1S6 2-OXAZOL-4-YL)CARBONYL]AMINO}-2-OXOETHYL]-1,3- HETNAM 3 1S6 THIAZOLIDINE-4-CARB OXYLIC ACID HETNAM NA SODIUM ION HETSYN 1S6 OXACILLIN, BOUND FORM FORMUL 2 1S6 C19 H21 N3 O5 S FORMUL 3 NA NA 1+ FORMUL 4 HOH *41(H2 O) HELIX 1 AA1 GLU A 115 THR A 117 5 3 HELIX 2 AA2 GLN A 118 ASP A 131 1 14 HELIX 3 AA3 GLU A 133 SER A 142 1 10 HELIX 4 AA4 PHE A 151 ASN A 156 1 6 HELIX 5 AA5 THR A 159 GLU A 171 1 13 HELIX 6 AA6 ALA A 194 GLY A 199 1 6 HELIX 7 AA7 SER A 217 LEU A 223 1 7 HELIX 8 AA8 LEU A 223 GLY A 229 1 7 HELIX 9 AA9 SER A 266 LYS A 285 1 20 HELIX 10 AB1 PRO A 335 THR A 338 5 4 HELIX 11 AB2 MET A 339 ASN A 350 1 12 HELIX 12 AB3 ASP A 373 GLY A 379 1 7 HELIX 13 AB4 PHE A 388 HIS A 394 1 7 HELIX 14 AB5 ASN A 397 GLY A 408 1 12 HELIX 15 AB6 GLY A 408 PHE A 419 1 12 HELIX 16 AB7 ASN A 441 SER A 448 1 8 HELIX 17 AB8 SER A 449 GLY A 451 5 3 HELIX 18 AB9 THR A 457 ASN A 470 1 14 HELIX 19 AC1 LYS A 505 ASP A 521 1 17 HELIX 20 AC2 SER A 596 ASN A 619 1 24 HELIX 21 AC3 SER A 645 ASN A 656 1 12 HELIX 22 AC4 THR A 703 LEU A 714 1 12 SHEET 1 AA1 6 PHE A 180 SER A 187 0 SHEET 2 AA1 6 PRO A 86 VAL A 96 -1 N SER A 93 O SER A 183 SHEET 3 AA1 6 ILE A 79 TYR A 80 -1 N ILE A 79 O ILE A 87 SHEET 4 AA1 6 ASP A 260 THR A 263 1 O THR A 263 N TYR A 80 SHEET 5 AA1 6 ILE A 480 ASP A 485 -1 O ALA A 482 N TYR A 262 SHEET 6 AA1 6 THR A 490 LYS A 493 -1 O THR A 490 N ASP A 485 SHEET 1 AA2 2 ALA A 98 VAL A 99 0 SHEET 2 AA2 2 GLN A 148 VAL A 149 -1 O VAL A 149 N ALA A 98 SHEET 1 AA3 2 ALA A 201 GLU A 205 0 SHEET 2 AA3 2 LYS A 211 GLY A 215 -1 O LEU A 214 N GLN A 202 SHEET 1 AA4 5 ILE A 301 ARG A 307 0 SHEET 2 AA4 5 TYR A 288 SER A 295 -1 N LEU A 293 O ALA A 303 SHEET 3 AA4 5 PHE A 583 GLN A 590 -1 O ILE A 584 N VAL A 294 SHEET 4 AA4 5 ILE A 569 SER A 576 -1 N ALA A 572 O VAL A 587 SHEET 5 AA4 5 ALA A 545 GLY A 549 -1 N GLY A 549 O SER A 571 SHEET 1 AA5 2 VAL A 358 PHE A 359 0 SHEET 2 AA5 2 MET A 386 THR A 387 -1 O MET A 386 N PHE A 359 SHEET 1 AA6 2 MET A 474 LEU A 475 0 SHEET 2 AA6 2 ILE A 498 GLY A 500 -1 O VAL A 499 N MET A 474 SHEET 1 AA7 2 MET A 527 TYR A 528 0 SHEET 2 AA7 2 LYS A 534 PRO A 535 -1 O LYS A 534 N TYR A 528 SHEET 1 AA8 3 GLN A 659 VAL A 663 0 SHEET 2 AA8 3 GLN A 685 SER A 690 1 O ILE A 688 N ILE A 661 SHEET 3 AA8 3 ILE A 669 SER A 672 -1 N LYS A 670 O LEU A 689 SHEET 1 AA9 3 GLU A 717 GLN A 721 0 SHEET 2 AA9 3 LYS A 743 GLY A 749 1 O LEU A 748 N GLN A 721 SHEET 3 AA9 3 THR A 726 GLN A 730 -1 N GLN A 728 O THR A 747 LINK OG SER A 337 C 1S6 A 801 1555 1555 1.46 CISPEP 1 LYS A 176 GLY A 177 0 9.99 CISPEP 2 ARG A 307 PRO A 308 0 -4.94 CISPEP 3 SER A 576 PRO A 577 0 -19.67 SITE 1 AC1 12 SER A 337 LYS A 340 TRP A 374 ASN A 377 SITE 2 AC1 12 SER A 395 ASN A 397 PHE A 450 GLN A 452 SITE 3 AC1 12 SER A 548 GLY A 549 THR A 550 GLN A 552 SITE 1 AC2 1 SER A 548 CRYST1 100.839 100.839 189.354 90.00 90.00 120.00 P 31 2 1 6 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 0.009917 0.005725 0.000000 0.00000 SCALE2 0.000000 0.011451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005281 0.00000