HEADER HYDROLASE 19-FEB-03 1NZO TITLE THE CRYSTAL STRUCTURE OF WILD TYPE PENICILLIN-BINDING PROTEIN 5 FROM TITLE 2 E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE FRACTION A, DD- COMPND 5 PEPTIDASE, DD-CARBOXYPEPTIDASE, PBP-5; COMPND 6 EC: 3.4.16.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DACA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: MC1061; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBR322 KEYWDS PEPTIDOGLYCAN SYNTHESIS, PENICILLIN-BINDING PROTEIN, DD- KEYWDS 2 CARBOXYPEPTIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.A.NICHOLAS,S.KRINGS,J.TOMBERG,G.NICOLA,C.DAVIES REVDAT 3 16-AUG-23 1NZO 1 REMARK REVDAT 2 24-FEB-09 1NZO 1 VERSN REVDAT 1 13-JAN-04 1NZO 0 JRNL AUTH R.A.NICHOLAS,S.KRINGS,J.TOMBERG,G.NICOLA,C.DAVIES JRNL TITL CRYSTAL STRUCTURE OF WILD-TYPE PENICILLIN-BINDING PROTEIN 5 JRNL TITL 2 FROM ESCHERICHIA COLI: IMPLICATIONS FOR DEACYLATION OF THE JRNL TITL 3 ACYL-ENZYME COMPLEX. JRNL REF J.BIOL.CHEM. V. 278 52826 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 14555648 JRNL DOI 10.1074/JBC.M310177200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.DAVIES,S.W.WHITE,R.A.NICHOLAS REMARK 1 TITL CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF REMARK 1 TITL 2 PENICILLIN-BINDING PROTEIN 5 AT 2.3-A RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 276 616 2001 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M004471200 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 30384 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1542 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1461 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2713 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : -0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.163 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.300 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2773 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3742 ; 1.509 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 351 ; 4.021 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 510 ;16.067 ;15.000 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): 415 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2088 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1254 ; 0.240 ; 0.300 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): 286 ; 0.195 ; 0.500 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): 52 ; 0.258 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.812 ; 0.500 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): 1739 ; 0.717 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2791 ; 1.294 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1034 ; 2.106 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 951 ; 3.264 ; 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 : NULL 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NZO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018393. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31624 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 54.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 1HD8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS PH 7.0, 8% PEG 400, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 54.67500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.67500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.14000 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 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 ASP A 1 REMARK 465 ASP A 2 REMARK 465 LEU A 3 REMARK 465 ASN A 356 REMARK 465 PHE A 357 REMARK 465 GLY A 358 REMARK 465 ASP A 359 REMARK 465 PRO A 360 REMARK 465 VAL A 361 REMARK 465 ILE A 362 REMARK 465 ASP A 363 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 HOH A 425 O HOH A 513 1.94 REMARK 500 O HOH A 505 O HOH A 529 2.04 REMARK 500 OD2 ASP A 24 OG1 THR A 265 2.09 REMARK 500 O ILE A 9 O HOH A 528 2.09 REMARK 500 O HOH A 446 O HOH A 474 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 5 NZ LYS A 62 1545 1.65 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 GLU A 65 CD GLU A 65 OE2 0.086 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 40 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 41 CB - CG - OD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 113 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 154 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 164 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 210 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 284 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 293 CB - CG - OD2 ANGL. DEV. = 6.4 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 ALA A 43 -134.01 54.75 REMARK 500 PRO A 81 -11.78 -46.13 REMARK 500 ASN A 208 68.70 -112.12 REMARK 500 ILE A 212 -54.07 -129.37 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 BME A 364 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 365 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NJ4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN- REMARK 900 BINDING PROTEIN 5 AT 1.9 A RESOLUTION REMARK 900 RELATED ID: 1HD8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN- REMARK 900 BINDING PROTEIN 5 AT 2.3 A RESOLUTION REMARK 900 RELATED ID: 1NZU RELATED DB: PDB REMARK 900 WILD-TYPE PENICILLIN-BINDING PROTEIN 5 FROM E. COLI MODIFIED BY REMARK 900 BETA-MERCAPTOETHANOL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5 REMARK 999 TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMOVED BY REMARK 999 DELETION OF THEIR RESPECTIVE CODONS, AN ADDITIONAL SIX REMARK 999 AMINO ACIDS (GDPVID) WERE INTRODUCED AT THE C TERMINUS DUE REMARK 999 TO READ-THROUGH TO THE STOP CODON. NONE OF THESE NON-NATIVE REMARK 999 RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY MAP. THE FIRST REMARK 999 29 AMINO ACIDS OF THE PROTEIN ENCODED BY THE OPEN READING REMARK 999 FRAME REPRESENT THE SIGNAL SEQUENCE, WHICH IS REMOVED DURING REMARK 999 MATURATION AND TRANSPORT TO THE PERIPLASMIC SPACE AND IS NOT REMARK 999 PRESENT IN THIS CONSTRUCT. DBREF 1NZO A 1 357 UNP P04287 DACA_ECOLI 30 386 SEQADV 1NZO GLY A 358 UNP P04287 SEE REMARK 999 SEQADV 1NZO ASP A 359 UNP P04287 SEE REMARK 999 SEQADV 1NZO PRO A 360 UNP P04287 SEE REMARK 999 SEQADV 1NZO VAL A 361 UNP P04287 SEE REMARK 999 SEQADV 1NZO ILE A 362 UNP P04287 SEE REMARK 999 SEQADV 1NZO ASP A 363 UNP P04287 SEE REMARK 999 SEQRES 1 A 363 ASP ASP LEU ASN ILE LYS THR MET ILE PRO GLY VAL PRO SEQRES 2 A 363 GLN ILE ASP ALA GLU SER TYR ILE LEU ILE ASP TYR ASN SEQRES 3 A 363 SER GLY LYS VAL LEU ALA GLU GLN ASN ALA ASP VAL ARG SEQRES 4 A 363 ARG ASP PRO ALA SER LEU THR LYS MET MET THR SER TYR SEQRES 5 A 363 VAL ILE GLY GLN ALA MET LYS ALA GLY LYS PHE LYS GLU SEQRES 6 A 363 THR ASP LEU VAL THR ILE GLY ASN ASP ALA TRP ALA THR SEQRES 7 A 363 GLY ASN PRO VAL PHE LYS GLY SER SER LEU MET PHE LEU SEQRES 8 A 363 LYS PRO GLY MET GLN VAL PRO VAL SER GLN LEU ILE ARG SEQRES 9 A 363 GLY ILE ASN LEU GLN SER GLY ASN ASP ALA CYS VAL ALA SEQRES 10 A 363 MET ALA ASP PHE ALA ALA GLY SER GLN ASP ALA PHE VAL SEQRES 11 A 363 GLY LEU MET ASN SER TYR VAL ASN ALA LEU GLY LEU LYS SEQRES 12 A 363 ASN THR HIS PHE GLN THR VAL HIS GLY LEU ASP ALA ASP SEQRES 13 A 363 GLY GLN TYR SER SER ALA ARG ASP MET ALA LEU ILE GLY SEQRES 14 A 363 GLN ALA LEU ILE ARG ASP VAL PRO ASN GLU TYR SER ILE SEQRES 15 A 363 TYR LYS GLU LYS GLU PHE THR PHE ASN GLY ILE ARG GLN SEQRES 16 A 363 LEU ASN ARG ASN GLY LEU LEU TRP ASP ASN SER LEU ASN SEQRES 17 A 363 VAL ASP GLY ILE LYS THR GLY HIS THR ASP LYS ALA GLY SEQRES 18 A 363 TYR ASN LEU VAL ALA SER ALA THR GLU GLY GLN MET ARG SEQRES 19 A 363 LEU ILE SER ALA VAL MET GLY GLY ARG THR PHE LYS GLY SEQRES 20 A 363 ARG GLU ALA GLU SER LYS LYS LEU LEU THR TRP GLY PHE SEQRES 21 A 363 ARG PHE PHE GLU THR VAL ASN PRO LEU LYS VAL GLY LYS SEQRES 22 A 363 GLU PHE ALA SER GLU PRO VAL TRP PHE GLY ASP SER ASP SEQRES 23 A 363 ARG ALA SER LEU GLY VAL ASP LYS ASP VAL TYR LEU THR SEQRES 24 A 363 ILE PRO ARG GLY ARG MET LYS ASP LEU LYS ALA SER TYR SEQRES 25 A 363 VAL LEU ASN SER SER GLU LEU HIS ALA PRO LEU GLN LYS SEQRES 26 A 363 ASN GLN VAL VAL GLY THR ILE ASN PHE GLN LEU ASP GLY SEQRES 27 A 363 LYS THR ILE GLU GLN ARG PRO LEU VAL VAL LEU GLN GLU SEQRES 28 A 363 ILE PRO GLU GLY ASN PHE GLY ASP PRO VAL ILE ASP HET BME A 364 4 HET BME A 365 4 HETNAM BME BETA-MERCAPTOETHANOL FORMUL 2 BME 2(C2 H6 O S) FORMUL 4 HOH *190(H2 O) HELIX 1 1 PRO A 42 SER A 44 5 3 HELIX 2 2 LEU A 45 ALA A 60 1 16 HELIX 3 3 GLY A 72 LYS A 84 5 13 HELIX 4 4 VAL A 99 LEU A 108 1 10 HELIX 5 5 GLY A 111 GLY A 124 1 14 HELIX 6 6 SER A 125 LEU A 140 1 16 HELIX 7 7 SER A 161 VAL A 176 1 16 HELIX 8 8 VAL A 176 SER A 181 1 6 HELIX 9 9 ILE A 182 GLU A 185 5 4 HELIX 10 10 ASN A 199 ASP A 204 5 6 HELIX 11 11 GLU A 249 PHE A 262 1 14 HELIX 12 12 ARG A 304 LEU A 308 5 5 SHEET 1 A 5 VAL A 30 GLN A 34 0 SHEET 2 A 5 ALA A 17 ASP A 24 -1 N LEU A 22 O LEU A 31 SHEET 3 A 5 ARG A 234 GLY A 242 -1 O ILE A 236 N ILE A 23 SHEET 4 A 5 GLY A 221 THR A 229 -1 N TYR A 222 O GLY A 242 SHEET 5 A 5 VAL A 209 THR A 217 -1 N THR A 217 O GLY A 221 SHEET 1 B 2 LEU A 68 THR A 70 0 SHEET 2 B 2 GLN A 96 PRO A 98 -1 O VAL A 97 N VAL A 69 SHEET 1 C 2 GLU A 187 PHE A 190 0 SHEET 2 C 2 ILE A 193 LEU A 196 -1 O GLN A 195 N PHE A 188 SHEET 1 D 2 PHE A 263 LEU A 269 0 SHEET 2 D 2 VAL A 296 PRO A 301 -1 O VAL A 296 N LEU A 269 SHEET 1 E 6 LYS A 309 LEU A 314 0 SHEET 2 E 6 VAL A 328 LEU A 336 -1 O GLN A 335 N LYS A 309 SHEET 3 E 6 LYS A 339 VAL A 348 -1 O ARG A 344 N ILE A 332 SHEET 4 E 6 ARG A 287 GLY A 291 -1 N GLY A 291 O VAL A 347 SHEET 5 E 6 ALA A 276 TRP A 281 -1 N ALA A 276 O LEU A 290 SHEET 6 E 6 LEU A 319 HIS A 320 1 O LEU A 319 N TRP A 281 CISPEP 1 GLY A 211 ILE A 212 0 4.00 CISPEP 2 ALA A 321 PRO A 322 0 5.13 SITE 1 AC1 2 LEU A 308 ALA A 310 SITE 1 AC2 4 TYR A 25 ASN A 26 GLN A 232 ARG A 234 CRYST1 109.350 50.280 84.530 90.00 120.90 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 0.009145 0.000000 0.005473 0.00000 SCALE2 0.000000 0.019887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013787 0.00000