HEADER HYDROLASE 16-NOV-07 3BEC TITLE CRYSTAL STRUCTURE OF E. COLI PENICILLIN-BINDING PROTEIN 5 IN COMPLEX TITLE 2 WITH A PEPTIDE-MIMETIC CEPHALOSPORIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 30-386; COMPND 5 SYNONYM: DD- PEPTIDASE, DD-CARBOXYPEPTIDASE, BETA-LACTAMASE, D- COMPND 6 ALANYL-D-ALANINE CARBOXYPEPTIDASE DACA, PBP-5; COMPND 7 EC: 3.4.16.4, 3.5.2.6; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 GENE: DACA, PFV; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: MC1061; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PBR322 KEYWDS PEPTIDOGLYCAN SYNTHESIS, PENICILLIN-BINDING PROTEIN, DD- KEYWDS 2 CARBOXYPEPTIDASE, HYDROLASE, DESIGNED CEPHALOSPORIN, CELL SHAPE, KEYWDS 3 CELL WALL BIOGENESIS/DEGRADATION, INNER MEMBRANE, MEMBRANE, PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR A.J.POWELL,C.DAVIES REVDAT 4 30-AUG-23 3BEC 1 REMARK LINK REVDAT 3 13-JUL-11 3BEC 1 VERSN REVDAT 2 24-FEB-09 3BEC 1 VERSN REVDAT 1 26-AUG-08 3BEC 0 JRNL AUTH E.SAUVAGE,A.J.POWELL,J.HEILEMANN,H.R.JOSEPHINE,P.CHARLIER, JRNL AUTH 2 C.DAVIES,R.F.PRATT JRNL TITL CRYSTAL STRUCTURES OF COMPLEXES OF BACTERIAL DD-PEPTIDASES JRNL TITL 2 WITH PEPTIDOGLYCAN-MIMETIC LIGANDS: THE SUBSTRATE JRNL TITL 3 SPECIFICITY PUZZLE JRNL REF J.MOL.BIOL. V. 381 383 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18602645 JRNL DOI 10.1016/J.JMB.2008.06.012 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 48813 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2602 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2901 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.3680 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 : 37 REMARK 3 SOLVENT ATOMS : 260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.70000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.68000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.538 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2834 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1926 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3821 ; 1.295 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4716 ; 0.872 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 351 ; 5.675 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;35.319 ;24.921 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 495 ;12.099 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;13.970 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 423 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3127 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 546 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 533 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1987 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1389 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1436 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 181 ; 0.148 ; 0.200 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): 4 ; 0.130 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 36 ; 0.194 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.137 ; 0.200 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): 1807 ; 1.137 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 723 ; 0.405 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2807 ; 1.646 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1179 ; 2.320 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1014 ; 3.276 ; 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): 5274 ; 1.546 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 260 ; 4.778 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4713 ; 2.323 ; 3.000 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 : 1.40 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 3BEC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045413. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR SI REMARK 200 -220 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51428 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 41.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1NZO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS PH 8.0, 8% PEG 400, VAPOR REMARK 280 DIFFUSION, SITTING 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 54.75000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.75000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.25000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 OG SER A 44 C7 HJ2 A 500 1.92 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 0.084 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 -138.67 52.30 REMARK 500 ASN A 208 69.11 -111.82 REMARK 500 ILE A 212 -61.84 -124.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 HJ2 A 500 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 364 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HJ2 A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 365 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 366 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 367 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BEB RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS' STATE THAT THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP REMARK 999 5, TERMED SPBP 5 TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMARK 999 REMOVED BY DELETION OF THEIR RESPECTIVE CODONS, AN ADDITIONAL SIX REMARK 999 AMINO ACIDS (GDPVID) WERE INTRODUCED AT THE C TERMINUS DUE TO READ- REMARK 999 THROUGH TO THE STOP CODON. NONE OF THESE NON-NATIVE RESIDUES ARE REMARK 999 VISIBLE IN THE ELECTRON DENSITY MAP. THE FIRST 29 AMINO ACIDS OF REMARK 999 THE PROTEIN ENCODED BY THE OPEN READING FRAME REPRESENT THE SIGNAL REMARK 999 SEQUENCE, WHICH IS REMOVED DURING MATURATION AND TRANSPORT TO THE REMARK 999 PERIPLASMIC SPACE AND IS NOT PRESENT IN THIS CONSTRUCT. DBREF 3BEC A 1 357 UNP P0AEB2 DACA_ECOLI 30 386 SEQADV 3BEC GLY A 358 UNP P0AEB2 SEE REMARK 999 SEQADV 3BEC ASP A 359 UNP P0AEB2 SEE REMARK 999 SEQADV 3BEC PRO A 360 UNP P0AEB2 SEE REMARK 999 SEQADV 3BEC VAL A 361 UNP P0AEB2 SEE REMARK 999 SEQADV 3BEC ILE A 362 UNP P0AEB2 SEE REMARK 999 SEQADV 3BEC ASP A 363 UNP P0AEB2 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 GOL A 364 6 HET HJ2 A 500 13 HET GOL A 365 6 HET GOL A 366 6 HET GOL A 367 6 HETNAM GOL GLYCEROL HETNAM HJ2 (2R)-2-[(R)-{[(6S)-6-AMINO-6- HETNAM 2 HJ2 CARBOXYHEXANOYL]AMINO}(CARBOXY)METHYL]-5-METHYL-3,6- HETNAM 3 HJ2 DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 4(C3 H8 O3) FORMUL 3 HJ2 C15 H23 N3 O7 S FORMUL 7 HOH *260(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 SER A 110 1 12 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 THR A 244 PHE A 262 1 19 HELIX 12 12 GLY A 303 LEU A 308 5 6 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 MET A 233 GLY A 242 -1 O ILE A 236 N ILE A 23 SHEET 4 A 5 GLY A 221 GLU A 230 -1 N TYR A 222 O GLY A 242 SHEET 5 A 5 VAL A 209 THR A 217 -1 N GLY A 215 O ASN A 223 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 LINK OG SER A 44 C8 HJ2 A 500 1555 1555 1.48 CISPEP 1 GLY A 211 ILE A 212 0 4.64 CISPEP 2 ALA A 321 PRO A 322 0 7.19 SITE 1 AC1 5 TYR A 52 TYR A 136 ALA A 139 LEU A 140 SITE 2 AC1 5 ASP A 175 SITE 1 AC2 8 ALA A 43 SER A 44 ARG A 198 THR A 214 SITE 2 AC2 8 GLY A 215 HIS A 216 PHE A 245 ARG A 248 SITE 1 AC3 10 ASN A 107 LEU A 108 TYR A 183 ASN A 197 SITE 2 AC3 10 ASN A 199 ILE A 212 LYS A 213 THR A 214 SITE 3 AC3 10 HOH A 528 HOH A 574 SITE 1 AC4 5 ASP A 74 ASN A 80 VAL A 116 GLN A 126 SITE 2 AC4 5 HIS A 151 SITE 1 AC5 7 TYR A 25 ASN A 26 GLN A 170 ARG A 174 SITE 2 AC5 7 TYR A 297 HOH A 597 HOH A 672 CRYST1 109.500 50.500 85.400 90.00 121.10 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 0.009132 0.000000 0.005509 0.00000 SCALE2 0.000000 0.019802 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013675 0.00000