HEADER PEPTIDE BINDING PROTEIN 05-FEB-09 2WAF TITLE PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE TITLE 2 (STRAIN R6) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 2B; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.-.- SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 171101; SOURCE 4 STRAIN: R6 KEYWDS PEPTIDOGLYCAN SYNTHESIS, PENICILLIN-BINDING PROTEIN, TRANSMEMBRANE, KEYWDS 2 ANTIBIOTIC RESISTANCE, CELL SHAPE, PEPTIDOGLYCAN, CELL MEMBRANE, KEYWDS 3 CELL WALL BIOGENESIS/DEGRADATION, MEMBRANE, INFECTION, RESISTANCE, KEYWDS 4 ANTIBIOTIC, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.CONTRERAS-MARTEL,C.DAHOUT-GONZALEZ,A.DOS-SANTOS-MARTINS,M.KOTNIK, AUTHOR 2 A.DESSEN REVDAT 6 13-DEC-23 2WAF 1 REMARK REVDAT 5 19-FEB-14 2WAF 1 REMARK REVDAT 4 13-JUL-11 2WAF 1 VERSN REVDAT 3 07-APR-09 2WAF 1 JRNL REVDAT 2 03-MAR-09 2WAF 1 JRNL REVDAT 1 24-FEB-09 2WAF 0 JRNL AUTH C.CONTRERAS-MARTEL,C.DAHOUT-GONZALEZ,A.DOS-SANTOS-MARTINS, JRNL AUTH 2 M.KOTNIK,A.DESSEN JRNL TITL PBP ACTIVE SITE FLEXIBILITY AS THE KEY MECHANISM FOR JRNL TITL 2 BETA-LACTAM RESISTANCE IN PNEUMOCOCCI JRNL REF J.MOL.BIOL. V. 387 899 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19233207 JRNL DOI 10.1016/J.JMB.2009.02.024 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.PAGLIERO,L.CHESNEL,J.HOPKINS,J.CROIZE,O.DIDEBERG,T.VERNET, REMARK 1 AUTH 2 A.DI-GUILMI REMARK 1 TITL BIOCHEMICAL CHARACTERIZATION OF STREPTOCOCCUS PNEUMONIAE REMARK 1 TITL 2 PENICILLIN-BINDING PROTEIN 2B AND ITS IMPLICATION IN REMARK 1 TITL 3 BETA-LACTAM RESISTANCE REMARK 1 REF ANTIMICROB.AGENTS CHEMOTHER. V. 48 1848 2004 REMARK 1 REFN ISSN 0066-4804 REMARK 1 PMID 15105143 REMARK 1 DOI 10.1128/AAC.48.5.1848-1855.2004 REMARK 2 REMARK 2 RESOLUTION. 3.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0067 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) : 3.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15012 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 770 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) : 3.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 747 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3560 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4701 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 69.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.67000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 4.71000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.57000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.538 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.532 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 78.151 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.867 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4785 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6501 ; 1.287 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 617 ; 7.344 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;37.541 ;26.039 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 794 ;19.993 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;18.503 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 747 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3612 ; 0.006 ; 0.021 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): 3065 ; 0.906 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4941 ; 1.781 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1720 ; 2.570 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1560 ; 4.636 ; 4.500 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 : NULL 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 86 A 185 REMARK 3 RESIDUE RANGE : A 196 A 213 REMARK 3 ORIGIN FOR THE GROUP (A): 18.4994 -5.6885 -43.4724 REMARK 3 T TENSOR REMARK 3 T11: 0.0023 T22: 0.5369 REMARK 3 T33: -0.2120 T12: 0.0149 REMARK 3 T13: 0.1925 T23: -0.1430 REMARK 3 L TENSOR REMARK 3 L11: 5.7758 L22: 9.8147 REMARK 3 L33: 5.7870 L12: 3.7165 REMARK 3 L13: 0.2679 L23: -1.9574 REMARK 3 S TENSOR REMARK 3 S11: -0.1840 S12: 0.6486 S13: 0.0543 REMARK 3 S21: -0.4826 S22: -0.1728 S23: -0.6567 REMARK 3 S31: -0.2666 S32: 0.1321 S33: 0.3568 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 52 A 85 REMARK 3 RESIDUE RANGE : A 186 A 195 REMARK 3 RESIDUE RANGE : A 214 A 310 REMARK 3 RESIDUE RANGE : A 548 A 566 REMARK 3 ORIGIN FOR THE GROUP (A): -0.0363 -15.0495 -19.7435 REMARK 3 T TENSOR REMARK 3 T11: -0.0009 T22: 0.0490 REMARK 3 T33: 0.0771 T12: -0.0076 REMARK 3 T13: 0.0294 T23: -0.0860 REMARK 3 L TENSOR REMARK 3 L11: 10.1276 L22: 0.4007 REMARK 3 L33: 2.7893 L12: 1.3193 REMARK 3 L13: -3.8873 L23: 0.0384 REMARK 3 S TENSOR REMARK 3 S11: -0.4412 S12: 0.2978 S13: -0.8039 REMARK 3 S21: -0.1814 S22: 0.1239 S23: -0.0598 REMARK 3 S31: 0.4606 S32: 0.2848 S33: 0.3172 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 311 A 547 REMARK 3 RESIDUE RANGE : A 567 A 682 REMARK 3 ORIGIN FOR THE GROUP (A): -32.3311 0.8373 4.2958 REMARK 3 T TENSOR REMARK 3 T11: -0.5965 T22: -0.6228 REMARK 3 T33: -0.3896 T12: -0.0487 REMARK 3 T13: -0.0618 T23: 0.1172 REMARK 3 L TENSOR REMARK 3 L11: 6.0374 L22: 2.6440 REMARK 3 L33: 5.2117 L12: -0.9879 REMARK 3 L13: -0.6026 L23: 1.1196 REMARK 3 S TENSOR REMARK 3 S11: -0.2301 S12: -0.1120 S13: 0.5100 REMARK 3 S21: 0.0743 S22: 0.2196 S23: -0.2126 REMARK 3 S31: -0.5154 S32: -0.0200 S33: 0.0105 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 2WAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1290038705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9312 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14291 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.290 REMARK 200 RESOLUTION RANGE LOW (A) : 47.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44000 REMARK 200 FOR SHELL : 2.820 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 2WAD REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M (NH4)2SO4, PH 8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 96.94850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.79650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 96.94850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.79650 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 LYS A 3 REMARK 465 PHE A 4 REMARK 465 ASN A 5 REMARK 465 SER A 6 REMARK 465 HIS A 7 REMARK 465 SER A 8 REMARK 465 ILE A 9 REMARK 465 PRO A 10 REMARK 465 ILE A 11 REMARK 465 ARG A 12 REMARK 465 LEU A 13 REMARK 465 ASN A 14 REMARK 465 LEU A 15 REMARK 465 LEU A 16 REMARK 465 PHE A 17 REMARK 465 SER A 18 REMARK 465 ILE A 19 REMARK 465 VAL A 20 REMARK 465 ILE A 21 REMARK 465 LEU A 22 REMARK 465 LEU A 23 REMARK 465 PHE A 24 REMARK 465 MET A 25 REMARK 465 THR A 26 REMARK 465 ILE A 27 REMARK 465 ILE A 28 REMARK 465 GLY A 29 REMARK 465 ARG A 30 REMARK 465 LEU A 31 REMARK 465 LEU A 32 REMARK 465 TYR A 33 REMARK 465 MET A 34 REMARK 465 GLN A 35 REMARK 465 VAL A 36 REMARK 465 LEU A 37 REMARK 465 ASN A 38 REMARK 465 LYS A 39 REMARK 465 ASP A 40 REMARK 465 PHE A 41 REMARK 465 TYR A 42 REMARK 465 GLU A 43 REMARK 465 LYS A 44 REMARK 465 LYS A 45 REMARK 465 LEU A 46 REMARK 465 ALA A 47 REMARK 465 SER A 48 REMARK 465 ALA A 49 REMARK 465 SER A 50 REMARK 465 GLN A 51 REMARK 465 GLU A 137 REMARK 465 LYS A 138 REMARK 465 ARG A 139 REMARK 465 LEU A 140 REMARK 465 ASP A 141 REMARK 465 SER A 142 REMARK 465 ASP A 143 REMARK 465 GLY A 144 REMARK 465 ASN A 145 REMARK 465 ARG A 146 REMARK 465 LEU A 147 REMARK 465 SER A 148 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 A 105 OD2 ASP A 195 1.65 REMARK 500 OE2 GLU A 113 CB SER A 163 1.74 REMARK 500 OG SER A 258 OD1 ASN A 260 1.85 REMARK 500 OG SER A 412 ND2 ASN A 422 1.95 REMARK 500 NE2 GLN A 416 O ASN A 463 1.96 REMARK 500 O VAL A 157 CG1 VAL A 160 1.98 REMARK 500 CG2 THR A 55 CB SER A 258 1.98 REMARK 500 OG SER A 209 O ILE A 215 1.99 REMARK 500 CG LYS A 283 O ASP A 297 2.01 REMARK 500 O LYS A 87 CG2 THR A 89 2.02 REMARK 500 O ALA A 246 N ALA A 249 2.02 REMARK 500 O THR A 52 CB GLU A 284 2.06 REMARK 500 CG2 THR A 55 OG SER A 258 2.07 REMARK 500 O VAL A 79 N SER A 218 2.11 REMARK 500 C SER A 105 OD2 ASP A 195 2.12 REMARK 500 O SER A 105 CG ASP A 195 2.14 REMARK 500 NE1 TRP A 221 NH2 ARG A 262 2.14 REMARK 500 O GLU A 171 N LYS A 173 2.15 REMARK 500 CG1 VAL A 80 CD1 ILE A 217 2.15 REMARK 500 N ILE A 54 O LYS A 283 2.16 REMARK 500 OE2 GLU A 169 NZ LYS A 172 2.17 REMARK 500 OD2 ASP A 288 OD1 ASN A 292 2.18 REMARK 500 O ILE A 106 CE LYS A 173 2.18 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 PRO A 196 C - N - CA ANGL. DEV. = 9.2 DEGREES REMARK 500 PRO A 652 C - N - CA ANGL. DEV. = 11.5 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 SER A 57 154.81 -42.59 REMARK 500 ALA A 59 129.27 -37.07 REMARK 500 LYS A 77 112.07 -171.76 REMARK 500 ARG A 84 -149.51 -127.39 REMARK 500 SER A 85 113.74 160.20 REMARK 500 ASN A 86 4.67 -50.38 REMARK 500 LYS A 87 -64.84 -106.27 REMARK 500 MET A 88 156.17 -48.11 REMARK 500 ALA A 90 -68.81 -23.30 REMARK 500 PRO A 109 77.57 -111.74 REMARK 500 ARG A 114 -30.86 -34.86 REMARK 500 GLU A 125 -75.83 -29.70 REMARK 500 ILE A 126 -69.49 -22.46 REMARK 500 GLN A 164 93.48 -66.75 REMARK 500 GLU A 171 -76.78 -39.10 REMARK 500 LYS A 172 -4.85 -35.18 REMARK 500 TYR A 176 -79.87 -54.49 REMARK 500 LEU A 177 -62.96 -23.67 REMARK 500 PHE A 187 -5.43 75.86 REMARK 500 THR A 191 -154.07 -109.49 REMARK 500 ILE A 192 89.87 -158.73 REMARK 500 ALA A 193 101.07 -50.11 REMARK 500 THR A 194 -143.49 -125.77 REMARK 500 PRO A 196 147.20 -21.52 REMARK 500 ASN A 198 -143.88 -79.97 REMARK 500 LYS A 210 5.31 -61.27 REMARK 500 PRO A 213 97.61 -18.14 REMARK 500 SER A 229 -33.94 -39.20 REMARK 500 GLU A 247 -81.60 -4.02 REMARK 500 ALA A 251 -29.44 -29.95 REMARK 500 ASP A 261 -176.20 -59.49 REMARK 500 TYR A 267 -153.87 58.08 REMARK 500 TYR A 272 33.96 -99.77 REMARK 500 GLU A 274 -72.21 -30.54 REMARK 500 LEU A 287 162.27 178.59 REMARK 500 SER A 295 142.02 142.51 REMARK 500 SER A 303 -162.18 -105.24 REMARK 500 LEU A 314 -70.91 -44.43 REMARK 500 ALA A 391 -50.19 -29.79 REMARK 500 GLN A 416 116.18 -33.93 REMARK 500 ILE A 434 130.25 -175.22 REMARK 500 PHE A 520 -84.95 -135.63 REMARK 500 ASN A 538 40.69 81.99 REMARK 500 LEU A 559 107.43 -39.20 REMARK 500 ASN A 572 162.60 173.01 REMARK 500 SER A 621 -154.20 150.44 REMARK 500 TYR A 622 153.38 -30.48 REMARK 500 VAL A 623 89.84 -177.40 REMARK 500 ALA A 624 -153.36 42.94 REMARK 500 ASP A 625 94.64 -62.81 REMARK 500 REMARK 500 THIS ENTRY HAS 57 RAMACHANDRAN OUTLIERS. 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 SER A 621 TYR A 622 148.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WAD RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS REMARK 900 PNEUMONIAE (STRAIN 5204) REMARK 900 RELATED ID: 2WAE RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS REMARK 900 PNEUMONIAE (STRAIN 5204) DBREF 2WAF A 1 680 UNP P0A3M6 PBP2_STRR6 1 680 DBREF 2WAF A 681 682 PDB 2WAF 2WAF 681 682 SEQRES 1 A 682 MET ARG LYS PHE ASN SER HIS SER ILE PRO ILE ARG LEU SEQRES 2 A 682 ASN LEU LEU PHE SER ILE VAL ILE LEU LEU PHE MET THR SEQRES 3 A 682 ILE ILE GLY ARG LEU LEU TYR MET GLN VAL LEU ASN LYS SEQRES 4 A 682 ASP PHE TYR GLU LYS LYS LEU ALA SER ALA SER GLN THR SEQRES 5 A 682 LYS ILE THR SER SER SER ALA ARG GLY GLU ILE TYR ASP SEQRES 6 A 682 ALA SER GLY LYS PRO LEU VAL GLU ASN THR LEU LYS GLN SEQRES 7 A 682 VAL VAL SER PHE THR ARG SER ASN LYS MET THR ALA THR SEQRES 8 A 682 ASP LEU LYS GLU THR ALA LYS LYS LEU LEU THR TYR VAL SEQRES 9 A 682 SER ILE SER SER PRO ASN LEU THR GLU ARG GLN LEU ALA SEQRES 10 A 682 ASP TYR TYR LEU ALA ASP PRO GLU ILE TYR LYS LYS ILE SEQRES 11 A 682 VAL GLU ALA LEU PRO SER GLU LYS ARG LEU ASP SER ASP SEQRES 12 A 682 GLY ASN ARG LEU SER GLU SER GLU LEU TYR ASN ASN ALA SEQRES 13 A 682 VAL ASP SER VAL GLN THR SER GLN LEU ASN TYR THR GLU SEQRES 14 A 682 ASP GLU LYS LYS GLU ILE TYR LEU PHE SER GLN LEU ASN SEQRES 15 A 682 ALA VAL GLY ASN PHE ALA THR GLY THR ILE ALA THR ASP SEQRES 16 A 682 PRO LEU ASN ASP SER GLN VAL ALA VAL ILE ALA SER ILE SEQRES 17 A 682 SER LYS GLU MET PRO GLY ILE SER ILE SER THR SER TRP SEQRES 18 A 682 ASP ARG LYS VAL LEU GLU THR SER LEU SER SER ILE VAL SEQRES 19 A 682 GLY SER VAL SER SER GLU LYS ALA GLY LEU PRO ALA GLU SEQRES 20 A 682 GLU ALA GLU ALA TYR LEU LYS LYS GLY TYR SER LEU ASN SEQRES 21 A 682 ASP ARG VAL GLY THR SER TYR LEU GLU LYS GLN TYR GLU SEQRES 22 A 682 GLU THR LEU GLN GLY LYS ARG SER VAL LYS GLU ILE HIS SEQRES 23 A 682 LEU ASP LYS TYR GLY ASN MET GLU SER VAL ASP THR ILE SEQRES 24 A 682 GLU GLU GLY SER LYS GLY ASN ASN ILE LYS LEU THR ILE SEQRES 25 A 682 ASP LEU ALA PHE GLN ASP SER VAL ASP ALA LEU LEU LYS SEQRES 26 A 682 SER TYR PHE ASN SER GLU LEU GLU ASN GLY GLY ALA LYS SEQRES 27 A 682 TYR SER GLU GLY VAL TYR ALA VAL ALA LEU ASN PRO LYS SEQRES 28 A 682 THR GLY ALA VAL LEU SER MET SER GLY ILE LYS HIS ASP SEQRES 29 A 682 LEU LYS THR GLY GLU LEU THR PRO ASP SER LEU GLY THR SEQRES 30 A 682 VAL THR ASN VAL PHE VAL PRO GLY SER VAL VAL LYS ALA SEQRES 31 A 682 ALA THR ILE SER SER GLY TRP GLU ASN GLY VAL LEU SER SEQRES 32 A 682 GLY ASN GLN THR LEU THR ASP GLN SER ILE VAL PHE GLN SEQRES 33 A 682 GLY SER ALA PRO ILE ASN SER TRP TYR THR GLN ALA TYR SEQRES 34 A 682 GLY SER PHE PRO ILE THR ALA VAL GLN ALA LEU GLU TYR SEQRES 35 A 682 SER SER ASN THR TYR MET VAL GLN THR ALA LEU GLY LEU SEQRES 36 A 682 MET GLY GLN THR TYR GLN PRO ASN MET PHE VAL GLY THR SEQRES 37 A 682 SER ASN LEU GLU SER ALA MET GLU LYS LEU ARG SER THR SEQRES 38 A 682 PHE GLY GLU TYR GLY LEU GLY THR ALA THR GLY ILE ASP SEQRES 39 A 682 LEU PRO ASP GLU SER THR GLY PHE VAL PRO LYS GLU TYR SEQRES 40 A 682 SER PHE ALA ASN TYR ILE THR ASN ALA PHE GLY GLN PHE SEQRES 41 A 682 ASP ASN TYR THR PRO MET GLN LEU ALA GLN TYR VAL ALA SEQRES 42 A 682 THR ILE ALA ASN ASN GLY VAL ARG VAL ALA PRO ARG ILE SEQRES 43 A 682 VAL GLU GLY ILE TYR GLY ASN ASN ASP LYS GLY GLY LEU SEQRES 44 A 682 GLY ASP LEU ILE GLN GLN LEU GLN PRO THR GLU MET ASN SEQRES 45 A 682 LYS VAL ASN ILE SER ASP SER ASP MET SER ILE LEU HIS SEQRES 46 A 682 GLN GLY PHE TYR GLN VAL ALA HIS GLY THR SER GLY LEU SEQRES 47 A 682 THR THR GLY ARG ALA PHE SER ASN GLY ALA LEU VAL SER SEQRES 48 A 682 ILE SER GLY LYS THR GLY THR ALA GLU SER TYR VAL ALA SEQRES 49 A 682 ASP GLY GLN GLN ALA THR ASN THR ASN ALA VAL ALA TYR SEQRES 50 A 682 ALA PRO SER ASP ASN PRO GLN ILE ALA VAL ALA VAL VAL SEQRES 51 A 682 PHE PRO HIS ASN THR ASN LEU THR ASN GLY VAL GLY PRO SEQRES 52 A 682 SER ILE ALA ARG ASP ILE ILE ASN LEU TYR GLN LYS TYR SEQRES 53 A 682 HIS PRO MET ASN HIS HIS HET CL A 700 1 HET CL A 701 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 2(CL 1-) FORMUL 4 HOH *11(H2 O) HELIX 1 1 THR A 89 THR A 102 1 14 HELIX 2 2 THR A 112 LEU A 121 1 10 HELIX 3 3 ASP A 123 GLU A 132 1 10 HELIX 4 4 GLU A 149 GLN A 161 1 13 HELIX 5 5 ASP A 170 ALA A 183 1 14 HELIX 6 6 ASP A 199 SER A 209 1 11 HELIX 7 7 LYS A 210 MET A 212 5 3 HELIX 8 8 LEU A 230 GLY A 235 1 6 HELIX 9 9 PRO A 245 GLY A 256 1 12 HELIX 10 10 TYR A 267 TYR A 272 1 6 HELIX 11 11 TYR A 272 GLN A 277 1 6 HELIX 12 12 ASP A 313 ASN A 334 1 22 HELIX 13 13 LEU A 375 ASN A 380 1 6 HELIX 14 14 PRO A 384 VAL A 387 5 4 HELIX 15 15 VAL A 388 ASN A 399 1 12 HELIX 16 16 ALA A 436 TYR A 442 1 7 HELIX 17 17 SER A 444 GLY A 457 1 14 HELIX 18 18 GLY A 467 SER A 469 5 3 HELIX 19 19 ASN A 470 TYR A 485 1 16 HELIX 20 20 SER A 508 ALA A 516 1 9 HELIX 21 21 THR A 524 ASN A 537 1 14 HELIX 22 22 SER A 577 GLY A 594 1 18 HELIX 23 23 GLY A 601 ASN A 606 1 6 HELIX 24 24 GLY A 660 LYS A 675 1 16 SHEET 1 AA 2 LYS A 53 SER A 58 0 SHEET 2 AA 2 GLY A 278 GLU A 284 -1 O GLY A 278 N SER A 58 SHEET 1 AB 4 ILE A 63 TYR A 64 0 SHEET 2 AB 4 ASN A 307 LEU A 310 1 O ILE A 308 N TYR A 64 SHEET 3 AB 4 VAL A 547 ASN A 553 -1 N GLU A 548 O LYS A 309 SHEET 4 AB 4 LEU A 559 GLN A 565 -1 N GLY A 560 O GLY A 552 SHEET 1 AC 3 THR A 189 GLY A 190 0 SHEET 2 AC 3 VAL A 72 THR A 83 -1 O PHE A 82 N GLY A 190 SHEET 3 AC 3 SER A 216 VAL A 225 -1 O SER A 216 N SER A 81 SHEET 1 AD 2 SER A 236 VAL A 237 0 SHEET 2 AD 2 GLY A 264 SER A 266 -1 N THR A 265 O SER A 236 SHEET 1 AE 2 HIS A 286 LEU A 287 0 SHEET 2 AE 2 MET A 293 SER A 295 -1 N GLU A 294 O HIS A 286 SHEET 1 AF 6 LEU A 370 PRO A 372 0 SHEET 2 AF 6 VAL A 355 HIS A 363 -1 O LYS A 362 N THR A 371 SHEET 3 AF 6 GLY A 342 LEU A 348 -1 O VAL A 343 N ILE A 361 SHEET 4 AF 6 ILE A 645 VAL A 650 -1 O ALA A 646 N LEU A 348 SHEET 5 AF 6 ALA A 634 ALA A 638 -1 O ALA A 634 N VAL A 649 SHEET 6 AF 6 SER A 613 THR A 616 -1 O SER A 613 N TYR A 637 SHEET 1 AG 2 THR A 407 ASP A 410 0 SHEET 2 AG 2 PHE A 432 THR A 435 -1 O PHE A 432 N ASP A 410 SHEET 1 AH 2 VAL A 540 VAL A 542 0 SHEET 2 AH 2 GLU A 570 LYS A 573 -1 N MET A 571 O ARG A 541 SHEET 1 AI 2 ALA A 619 SER A 621 0 SHEET 2 AI 2 ALA A 629 ASN A 631 -1 O ALA A 629 N SER A 621 CISPEP 1 GLY A 626 GLN A 627 0 11.78 CISPEP 2 ALA A 638 PRO A 639 0 -10.48 SITE 1 AC1 2 ASN A 656 THR A 658 SITE 1 AC2 1 ARG A 667 CRYST1 193.897 51.593 121.440 90.00 112.38 90.00 C 1 2 1 4 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 0.005157 0.000000 0.002124 0.00000 SCALE2 0.000000 0.019382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008905 0.00000