HEADER PEPTIDOGLYCAN 16-DEC-04 2BG3 OBSLTE 03-APR-07 2BG3 2UWX TITLE ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN TITLE 2 CLASS A PENICILLIN-BINDING PROTEINS (PBPS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRANSPEPTIDASE DOMAIN, RESIDUES 323-791; COMPND 5 SYNONYM: PBP1B; COMPND 6 EC: 2.4.1.129; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 STRAIN: R6; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYS; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS PEPTIDOGLYCAN SYNTHESIS MULTIFUNCTIONAL ENZYME, CELL WALL, KEYWDS 2 PEPTIDOGLYCAN EXPDTA X-RAY DIFFRACTION AUTHOR P.MACHEBOEUF,A.M.DI GUILMI,V.JOB,T.VERNET,O.DIDEBERG, AUTHOR 2 A.DESSEN REVDAT 1 26-OCT-05 2BG3 0 JRNL AUTH P.MACHEBOEUF,A.M.DI GUILMI,V.JOB,T.VERNET, JRNL AUTH 2 O.DIDEBERG,A.DESSEN JRNL TITL ACTIVE SITE RESTRUCTURING REGULATES LIGAND JRNL TITL 2 RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 577 2005 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 28153 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 SET) : 0.203 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2794 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3571 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 253 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.85000 REMARK 3 B22 (A**2) : 4.16000 REMARK 3 B33 (A**2) : -1.31000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.99 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 32.56 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : SERINE-NITRO.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : SERINE-NITRO.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BG3 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-01) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 20-DEC-2004. REMARK 100 THE EBI ID CODE IS EBI-21996. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-2004 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28153 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 19.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.03000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2BG1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM HEPES PH 7.0, 0.8M SO4(NH4)2, REMARK 280 2.8M NACL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,1/2+Z REMARK 290 3555 -X,Y,1/2-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 1/2+X,1/2+Y,Z REMARK 290 6555 1/2-X,1/2-Y,1/2+Z REMARK 290 7555 1/2-X,1/2+Y,1/2-Z REMARK 290 8555 1/2+X,1/2-Y,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.98800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.98800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 49.16550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 74.72350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.16550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 74.72350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.98800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.16550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 74.72350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.98800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.16550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 74.72350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, Z 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, ARG 336 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, 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 GLU A 317 REMARK 465 SER A 318 REMARK 465 ASP A 319 REMARK 465 MET A 320 REMARK 465 LEU A 321 REMARK 465 ARG A 322 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 GLN A 336 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 105 CG1 CG2 CD1 REMARK 470 ILE A 119 CG1 CG2 CD1 REMARK 470 LYS A 364 CG CD CE NZ REMARK 470 GLN A 444 CG CD OE1 NE2 REMARK 470 NC1 A 460 O REMARK 470 GLN A 601 CG CD OE1 NE2 REMARK 470 LYS A 603 CG CD CE NZ REMARK 470 GLN A 686 CG CD OE1 NE2 REMARK 470 LYS A 738 CG CD CE NZ REMARK 470 SER A 740 OG REMARK 470 LYS A 744 CG CD CE NZ REMARK 470 LYS A 760 CG CD CE NZ REMARK 470 SER A 789 OG REMARK 470 LEU A 790 CG CD1 CD2 REMARK 470 PRO A 791 CA C O CB CG CD 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 REMARK 500 O HOH Z 136 O HOH Z 138 1.75 REMARK 500 OG SER A 691 O HOH Z 204 2.03 REMARK 500 O20 NC1 A 460 O HOH Z 86 2.09 REMARK 500 O PRO A 458 OG1 THR A 461 2.16 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH Z 144 O HOH Z 144 3655 0.61 REMARK 500 CL CL A 1793 CL CL A 1793 3655 0.80 REMARK 500 OD1 ASP A 377 ND2 ASN A 714 6555 2.17 REMARK 500 OD2 ASP A 359 OG1 THR A 642 6555 2.19 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ILE A 108 CG1 ILE A 108 CD1 0.082 REMARK 500 ILE A 108 CB ILE A 108 CG2 -0.068 REMARK 500 THR A 114 CB THR A 114 CG2 0.072 REMARK 500 ARG A 358 CG ARG A 358 CD 0.071 REMARK 500 LYS A 367 CB LYS A 367 CG -0.071 REMARK 500 LYS A 367 CG LYS A 367 CD -0.086 REMARK 500 LYS A 367 CD LYS A 367 CE -0.088 REMARK 500 ALA A 459 N ALA A 459 CA 0.098 REMARK 500 ALA A 459 CA ALA A 459 C 0.078 REMARK 500 ALA A 459 C NC1 A 460 N -0.345 REMARK 500 NC1 A 460 C THR A 461 N 0.060 REMARK 500 THR A 462 C LYS A 463 N 0.068 REMARK 500 LEU A 790 C PRO A 791 N -0.086 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER A 111 CA - CB - OG ANGL. DEV. =-14.7 DEGREES REMARK 500 ASP A 112 CB - CG - OD1 ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 358 CG - CD - NE ANGL. DEV. =-17.4 DEGREES REMARK 500 ARG A 358 CD - NE - CZ ANGL. DEV. = 9.6 DEGREES REMARK 500 LYS A 367 CD - CE - NZ ANGL. DEV. = -9.4 DEGREES REMARK 500 ARG A 376 CG - CD - NE ANGL. DEV. =-11.7 DEGREES REMARK 500 ALA A 459 N - CA - C ANGL. DEV. = 10.0 DEGREES REMARK 500 ALA A 459 C - N - CA ANGL. DEV. = 10.4 DEGREES REMARK 500 NC1 A 460 C - N - CA ANGL. DEV. = 32.0 DEGREES REMARK 500 THR A 461 C - N - CA ANGL. DEV. = 17.4 DEGREES REMARK 500 TYR A 498 N - CA - C ANGL. DEV. =-11.5 DEGREES REMARK 500 THR A 667 N - CA - C ANGL. DEV. =-13.6 DEGREES REMARK 500 PHE A 717 N - CA - C ANGL. DEV. =-10.0 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 ALA A 499 -115.17 72.05 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 ALA A 459 NC1 A 460 132.56 REMARK 500 NC1 A 460 THR A 461 132.15 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH Z 90 DISTANCE = 5.82 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 SITE_DESCRIPTION: SO4 BINDING SITE FOR CHAIN A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 SITE_DESCRIPTION: CL BINDING SITE FOR CHAIN A REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BG1 RELATED DB: PDB REMARK 900 ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN REMARK 900 CLASS A PENICILLIN-BINDING PROTEINS (PBPS) REMARK 900 RELATED ID: 2BG4 RELATED DB: PDB REMARK 900 ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN REMARK 900 CLASS A PENICILLIN-BINDING PROTEINS (PBPS) DBREF 2BG3 A 101 125 UNP O70038 O70038 101 125 DBREF 2BG3 A 323 791 UNP O70038 O70038 323 791 SEQADV 2BG3 GLN A 686 UNP O70038 ARG 686 ENGINEERED MUTATION SEQADV 2BG3 GLN A 687 UNP O70038 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 MET LEU ARG GLN SEQRES 3 A 494 ASP PHE LEU PRO SER GLY THR VAL THR GLY ILE SER GLN 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 NC1 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 ASN 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 MODRES 2BG3 NC1 A 460 SER NITROCEFIN ACYL-SERINE HET NC1 A 460 41 HET SO4 A1791 5 HET CL A1792 1 HET CL A1793 1 HETNAM NC1 NITROCEFIN ACYL-SERINE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 1 NC1 C24 H21 N5 O11 S2 2- FORMUL 2 SO4 O4 S 2- FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *253(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 ASN A 385 1 18 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 THR A 462 ALA A 467 1 6 HELIX 7 7 ALA A 467 GLN A 474 1 8 HELIX 8 8 LEU A 509 SER A 516 1 8 HELIX 9 9 ASN A 518 ASN A 531 1 14 HELIX 10 10 ASP A 534 MET A 542 1 9 HELIX 11 11 SER A 553 GLY A 557 5 5 HELIX 12 12 THR A 563 ASN A 576 1 14 HELIX 13 13 SER A 609 SER A 626 1 18 HELIX 14 14 THR A 631 ASN A 640 1 10 HELIX 15 15 ASN A 640 ASN A 645 1 6 HELIX 16 16 ASN A 656 ASP A 658 5 3 HELIX 17 17 SER A 691 SER A 708 1 18 HELIX 18 18 SER A 775 LEU A 790 1 16 SHEET 1 AA 5 VAL A 115 ALA A 117 0 SHEET 2 AA 5 GLU A 107 THR A 109 -1 O ILE A 108 N ILE A 116 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 GLY A 737 SER A 740 0 SHEET 2 AF 2 GLU A 745 VAL A 748 -1 O VAL A 746 N VAL A 739 LINK C ALA A 459 N NC1 A 460 LINK C NC1 A 460 N THR A 461 SITE 1 AC1 6 THR A 563 LYS A 583 HOH Z 146 HOH Z 251 SITE 2 AC1 6 HOH Z 252 HOH Z 253 SITE 1 AC3 1 SER A 634 CRYST1 98.331 149.447 97.976 90.00 90.00 90.00 C 2 2 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 0.010170 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010207 0.00000