HEADER BIOSYNTHETIC PROTEIN 02-NOV-07 2ZC5 TITLE PENICILLIN-BINDING PROTEIN 1A (PBP 1A) ACYL-ENZYME COMPLEX (BIAPENEM) TITLE 2 FROM STREPTOCOCCUS PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 1A; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 47-70; COMPND 5 SYNONYM: PBP-1A, EXPORTED PROTEIN 2; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: TRANSGLYCOSYLASE DOMAIN; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PENICILLIN-BINDING PROTEIN 1A; COMPND 10 CHAIN: B, D; COMPND 11 FRAGMENT: UNP RESIDUES 264-653; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES; COMPND 14 OTHER_DETAILS: TRANSPEPTIDASE DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 GENE: PBPA, EXP2; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 9 GENE: PBP1A; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1 KEYWDS PEPTIDOGLYCAN SYNTHESIS, CELL WALL, PENICILLIN-BINDING, ANTIBIOTICS, KEYWDS 2 BIAPENEM, ANTIBIOTIC RESISTANCE, CELL SHAPE, CELL WALL KEYWDS 3 BIOGENESIS/DEGRADATION, MULTIFUNCTIONAL ENZYME, SECRETED, KEYWDS 4 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.YAMADA,T.WATANABE,Y.TAKEUCHI REVDAT 6 30-OCT-24 2ZC5 1 REMARK REVDAT 5 01-NOV-23 2ZC5 1 REMARK REVDAT 4 10-NOV-21 2ZC5 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK REVDAT 3 24-FEB-09 2ZC5 1 VERSN REVDAT 2 03-JUN-08 2ZC5 1 JRNL REVDAT 1 08-APR-08 2ZC5 0 JRNL AUTH M.YAMADA,T.WATANABE,N.BABA,Y.TAKEUCHI,F.OHSAWA,S.GOMI JRNL TITL CRYSTAL STRUCTURES OF BIAPENEM AND TEBIPENEM COMPLEXED WITH JRNL TITL 2 PENICILLIN-BINDING PROTEINS 2X AND 1A FROM STREPTOCOCCUS JRNL TITL 3 PNEUMONIAE JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 52 2053 2008 JRNL REFN ISSN 0066-4804 JRNL PMID 18391040 JRNL DOI 10.1128/AAC.01456-07 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.1 REMARK 3 NUMBER OF REFLECTIONS : 18139 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 977 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1322 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.3160 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6300 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.74000 REMARK 3 B22 (A**2) : 0.97000 REMARK 3 B33 (A**2) : 2.77000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.521 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.377 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.096 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.868 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6504 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8861 ; 1.010 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 796 ; 5.407 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 315 ;36.738 ;25.175 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1016 ;16.506 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;19.016 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 956 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5058 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2868 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4409 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 191 ; 0.135 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.114 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 52 ; 0.234 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.125 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 4 ; 0.156 ; 0.200 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): 4043 ; 0.305 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6391 ; 0.553 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2853 ; 0.461 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2470 ; 0.839 ; 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 : 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 2ZC5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000027785. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED DOUBLE-CRYSTAL REMARK 200 OPTICS : ROTATED-INCLINED DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR, RHODIUM-COATED REMARK 200 HORIZONTAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19127 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.1 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2ZC6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.004-0.006M ZINC SULFATE, 0.05M MES, REMARK 280 PH6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 92.85200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.33250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 92.85200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.33250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 LEU A 47 REMARK 465 VAL A 48 REMARK 465 ALA A 49 REMARK 465 THR A 50 REMARK 465 GLY A 67 REMARK 465 SER A 68 REMARK 465 GLU A 69 REMARK 465 ARG A 70 REMARK 465 SER B 264 REMARK 465 ALA B 265 REMARK 465 SER B 266 REMARK 465 GLY B 651 REMARK 465 ALA B 652 REMARK 465 ARG B 653 REMARK 465 LEU C 47 REMARK 465 VAL C 48 REMARK 465 ALA C 49 REMARK 465 THR C 50 REMARK 465 GLY C 67 REMARK 465 SER C 68 REMARK 465 GLU C 69 REMARK 465 ARG C 70 REMARK 465 SER D 264 REMARK 465 ALA D 265 REMARK 465 SER D 266 REMARK 465 GLY D 651 REMARK 465 ALA D 652 REMARK 465 ARG D 653 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 THR A 51 OG1 CG2 REMARK 470 LYS A 59 NZ REMARK 470 ASP B 317 CG OD1 OD2 REMARK 470 THR C 51 OG1 CG2 REMARK 470 LYS C 59 NZ REMARK 470 ASP D 317 CG OD1 OD2 REMARK 470 GLU D 638 CG CD OE1 OE2 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 60 7.77 87.45 REMARK 500 THR B 316 -167.03 -129.29 REMARK 500 HIS B 349 90.13 64.23 REMARK 500 GLN B 350 72.52 -116.61 REMARK 500 SER B 351 22.38 -72.50 REMARK 500 ASP B 396 76.66 -110.88 REMARK 500 SER B 428 68.57 61.58 REMARK 500 GLU B 471 -76.00 -98.72 REMARK 500 SER B 472 16.09 55.90 REMARK 500 LYS B 474 -106.66 -140.92 REMARK 500 ASP B 509 22.86 -73.89 REMARK 500 LYS B 649 -158.05 -86.66 REMARK 500 ASP D 324 -171.60 -173.06 REMARK 500 ASN D 338 -15.27 -153.07 REMARK 500 SER D 351 87.33 -66.05 REMARK 500 ASP D 396 78.08 -102.49 REMARK 500 PRO D 402 119.03 -28.84 REMARK 500 ASN D 468 106.54 -56.49 REMARK 500 GLU D 471 -58.01 -142.85 REMARK 500 SER D 472 -8.70 69.08 REMARK 500 LYS D 474 -102.85 -132.48 REMARK 500 THR D 560 87.52 -157.36 REMARK 500 LYS D 573 73.90 -109.03 REMARK 500 THR D 588 -156.67 -112.61 REMARK 500 ASN D 643 76.94 -158.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 395 ND1 REMARK 620 2 GLU B 435 OE1 128.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 808 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU D 318 OE2 REMARK 620 2 TYR D 319 OH 107.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 806 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 395 ND1 REMARK 620 2 GLU D 435 OE2 111.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 808 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMG B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMG D 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZC3 RELATED DB: PDB REMARK 900 RELATED ID: 2ZC4 RELATED DB: PDB REMARK 900 RELATED ID: 2ZC6 RELATED DB: PDB DBREF 2ZC5 A 47 70 UNP Q8DR59 PBPA_STRR6 47 70 DBREF 2ZC5 B 264 653 UNP Q549Y6 Q549Y6_STRPN 264 653 DBREF 2ZC5 C 47 70 UNP Q8DR59 PBPA_STRR6 47 70 DBREF 2ZC5 D 264 653 UNP Q549Y6 Q549Y6_STRPN 264 653 SEQADV 2ZC5 GLN B 545 UNP Q549Y6 ARG 545 ENGINEERED MUTATION SEQADV 2ZC5 GLN D 545 UNP Q549Y6 ARG 545 ENGINEERED MUTATION SEQRES 1 A 24 LEU VAL ALA THR THR SER SER LYS ILE TYR ASP ASN LYS SEQRES 2 A 24 ASN GLN LEU ILE ALA ASP LEU GLY SER GLU ARG SEQRES 1 B 390 SER ALA SER ASN TYR PRO ALA TYR MET ASP ASN TYR LEU SEQRES 2 B 390 LYS GLU VAL ILE ASN GLN VAL GLU GLU GLU THR GLY TYR SEQRES 3 B 390 ASN LEU LEU THR THR GLY MET ASP VAL TYR THR ASN VAL SEQRES 4 B 390 ASP GLN GLU ALA GLN LYS HIS LEU TRP ASP ILE TYR ASN SEQRES 5 B 390 THR ASP GLU TYR VAL ALA TYR PRO ASP ASP GLU LEU GLN SEQRES 6 B 390 VAL ALA SER THR ILE VAL ASP VAL SER ASN GLY LYS VAL SEQRES 7 B 390 ILE ALA GLN LEU GLY ALA ARG HIS GLN SER SER ASN VAL SEQRES 8 B 390 SER PHE GLY ILE ASN GLN ALA VAL GLU THR ASN ARG ASP SEQRES 9 B 390 TRP GLY SER THR MET LYS PRO ILE THR ASP TYR ALA PRO SEQRES 10 B 390 ALA LEU GLU TYR GLY VAL TYR ASP SER THR ALA THR ILE SEQRES 11 B 390 VAL HIS ASP GLU PRO TYR ASN TYR PRO GLY THR ASN THR SEQRES 12 B 390 PRO VAL TYR ASN TRP ASP ARG GLY TYR PHE GLY ASN ILE SEQRES 13 B 390 THR LEU GLN TYR ALA LEU GLN GLN SER ARG ASN VAL PRO SEQRES 14 B 390 ALA VAL GLU THR LEU ASN LYS VAL GLY LEU ASN ARG ALA SEQRES 15 B 390 LYS THR PHE LEU ASN GLY LEU GLY ILE ASP TYR PRO SER SEQRES 16 B 390 ILE HIS TYR SER ASN ALA ILE SER SER ASN THR THR GLU SEQRES 17 B 390 SER ASP LYS LYS TYR GLY ALA SER SER GLU LYS MET ALA SEQRES 18 B 390 ALA ALA TYR ALA ALA PHE ALA ASN GLY GLY THR TYR TYR SEQRES 19 B 390 LYS PRO MET TYR ILE HIS LYS VAL VAL PHE SER ASP GLY SEQRES 20 B 390 SER GLU LYS GLU PHE SER ASN VAL GLY THR ARG ALA MET SEQRES 21 B 390 LYS GLU THR THR ALA TYR MET MET THR ASP MET MET LYS SEQRES 22 B 390 THR VAL LEU SER TYR GLY THR GLY GLN ASN ALA TYR LEU SEQRES 23 B 390 ALA TRP LEU PRO GLN ALA GLY LYS THR GLY THR SER ASN SEQRES 24 B 390 TYR THR ASP GLU GLU ILE GLU ASN HIS ILE LYS THR SER SEQRES 25 B 390 GLN PHE VAL ALA PRO ASP GLU LEU PHE ALA GLY TYR THR SEQRES 26 B 390 ARG LYS TYR SER MET ALA VAL TRP THR GLY TYR SER ASN SEQRES 27 B 390 ARG LEU THR PRO LEU VAL GLY ASN GLY LEU THR VAL ALA SEQRES 28 B 390 ALA LYS VAL TYR ARG SER MET MET THR TYR LEU SER GLU SEQRES 29 B 390 GLY SER ASN PRO GLU ASP TRP ASN ILE PRO GLU GLY LEU SEQRES 30 B 390 TYR ARG ASN GLY GLU PHE VAL PHE LYS ASN GLY ALA ARG SEQRES 1 C 24 LEU VAL ALA THR THR SER SER LYS ILE TYR ASP ASN LYS SEQRES 2 C 24 ASN GLN LEU ILE ALA ASP LEU GLY SER GLU ARG SEQRES 1 D 390 SER ALA SER ASN TYR PRO ALA TYR MET ASP ASN TYR LEU SEQRES 2 D 390 LYS GLU VAL ILE ASN GLN VAL GLU GLU GLU THR GLY TYR SEQRES 3 D 390 ASN LEU LEU THR THR GLY MET ASP VAL TYR THR ASN VAL SEQRES 4 D 390 ASP GLN GLU ALA GLN LYS HIS LEU TRP ASP ILE TYR ASN SEQRES 5 D 390 THR ASP GLU TYR VAL ALA TYR PRO ASP ASP GLU LEU GLN SEQRES 6 D 390 VAL ALA SER THR ILE VAL ASP VAL SER ASN GLY LYS VAL SEQRES 7 D 390 ILE ALA GLN LEU GLY ALA ARG HIS GLN SER SER ASN VAL SEQRES 8 D 390 SER PHE GLY ILE ASN GLN ALA VAL GLU THR ASN ARG ASP SEQRES 9 D 390 TRP GLY SER THR MET LYS PRO ILE THR ASP TYR ALA PRO SEQRES 10 D 390 ALA LEU GLU TYR GLY VAL TYR ASP SER THR ALA THR ILE SEQRES 11 D 390 VAL HIS ASP GLU PRO TYR ASN TYR PRO GLY THR ASN THR SEQRES 12 D 390 PRO VAL TYR ASN TRP ASP ARG GLY TYR PHE GLY ASN ILE SEQRES 13 D 390 THR LEU GLN TYR ALA LEU GLN GLN SER ARG ASN VAL PRO SEQRES 14 D 390 ALA VAL GLU THR LEU ASN LYS VAL GLY LEU ASN ARG ALA SEQRES 15 D 390 LYS THR PHE LEU ASN GLY LEU GLY ILE ASP TYR PRO SER SEQRES 16 D 390 ILE HIS TYR SER ASN ALA ILE SER SER ASN THR THR GLU SEQRES 17 D 390 SER ASP LYS LYS TYR GLY ALA SER SER GLU LYS MET ALA SEQRES 18 D 390 ALA ALA TYR ALA ALA PHE ALA ASN GLY GLY THR TYR TYR SEQRES 19 D 390 LYS PRO MET TYR ILE HIS LYS VAL VAL PHE SER ASP GLY SEQRES 20 D 390 SER GLU LYS GLU PHE SER ASN VAL GLY THR ARG ALA MET SEQRES 21 D 390 LYS GLU THR THR ALA TYR MET MET THR ASP MET MET LYS SEQRES 22 D 390 THR VAL LEU SER TYR GLY THR GLY GLN ASN ALA TYR LEU SEQRES 23 D 390 ALA TRP LEU PRO GLN ALA GLY LYS THR GLY THR SER ASN SEQRES 24 D 390 TYR THR ASP GLU GLU ILE GLU ASN HIS ILE LYS THR SER SEQRES 25 D 390 GLN PHE VAL ALA PRO ASP GLU LEU PHE ALA GLY TYR THR SEQRES 26 D 390 ARG LYS TYR SER MET ALA VAL TRP THR GLY TYR SER ASN SEQRES 27 D 390 ARG LEU THR PRO LEU VAL GLY ASN GLY LEU THR VAL ALA SEQRES 28 D 390 ALA LYS VAL TYR ARG SER MET MET THR TYR LEU SER GLU SEQRES 29 D 390 GLY SER ASN PRO GLU ASP TRP ASN ILE PRO GLU GLY LEU SEQRES 30 D 390 TYR ARG ASN GLY GLU PHE VAL PHE LYS ASN GLY ALA ARG HET ZN B 801 1 HET ZN B 802 1 HET ZN B 803 1 HET ZN B 804 1 HET BMG B 701 24 HET ZN D 805 1 HET ZN D 806 1 HET ZN D 807 1 HET ZN D 808 1 HET BMG D 701 24 HETNAM ZN ZINC ION HETNAM BMG (4R,5S)-3-(6,7-DIHYDRO-5H-PYRAZOLO[1,2-A][1,2, HETNAM 2 BMG 4]TRIAZOL-4-IUM-6-YLSULFANYL)-5-[(1S,2R)-1-FORMYL-2- HETNAM 3 BMG HYDROXYPROPYL]-4-METH YL-4,5-DIHYDRO-1H-PYRROLE-2- HETNAM 4 BMG CARBOXYLATE HETSYN BMG (4R,5S)-3-(6,7-DIHYDRO-5H-PYRAZOLO[1,2-A][1,2, HETSYN 2 BMG 4]TRIAZOL-4-IUM-6-YLTHIO)-5-((2S,3R)-3-HYDROXY-1- HETSYN 3 BMG OXOBUTAN-2-YL)-4- METHYL-4,5-DIHYDRO-1H-PYRROLE-2- HETSYN 4 BMG CARBOXYLATE FORMUL 5 ZN 8(ZN 2+) FORMUL 9 BMG 2(C15 H20 N4 O4 S) FORMUL 15 HOH *6(H2 O) HELIX 1 1 MET B 272 THR B 287 1 16 HELIX 2 2 ASP B 303 ASN B 315 1 13 HELIX 3 3 TRP B 368 SER B 370 5 3 HELIX 4 4 THR B 371 ASP B 377 1 7 HELIX 5 5 ASP B 377 TYR B 384 1 8 HELIX 6 6 LEU B 421 GLN B 427 1 7 HELIX 7 7 ARG B 429 GLY B 441 1 13 HELIX 8 8 GLY B 441 GLY B 451 1 11 HELIX 9 9 HIS B 460 SER B 466 5 7 HELIX 10 10 SER B 479 GLY B 493 1 15 HELIX 11 11 LYS B 524 GLY B 542 1 19 HELIX 12 12 THR B 543 TYR B 548 5 6 HELIX 13 13 THR B 564 HIS B 571 1 8 HELIX 14 14 ASN B 609 LEU B 611 5 3 HELIX 15 15 THR B 612 GLU B 627 1 16 HELIX 16 16 PRO D 269 TYR D 271 5 3 HELIX 17 17 MET D 272 GLY D 288 1 17 HELIX 18 18 ASP D 303 THR D 316 1 14 HELIX 19 19 TRP D 368 THR D 371 5 4 HELIX 20 20 MET D 372 ASP D 377 1 6 HELIX 21 21 ASP D 377 TYR D 384 1 8 HELIX 22 22 LEU D 421 GLN D 427 1 7 HELIX 23 23 ARG D 429 GLY D 441 1 13 HELIX 24 24 GLY D 441 LEU D 452 1 12 HELIX 25 25 HIS D 460 ILE D 465 5 6 HELIX 26 26 SER D 479 ASN D 492 1 14 HELIX 27 27 LYS D 524 LEU D 539 1 16 HELIX 28 28 THR D 564 HIS D 571 1 8 HELIX 29 29 ASN D 609 LEU D 611 5 3 HELIX 30 30 THR D 612 GLU D 627 1 16 SHEET 1 A 5 LEU A 62 ASP A 65 0 SHEET 2 A 5 LYS A 54 TYR A 56 -1 N ILE A 55 O ALA A 64 SHEET 3 A 5 MET B 296 THR B 300 1 O THR B 300 N TYR A 56 SHEET 4 A 5 ILE B 502 PHE B 507 -1 O HIS B 503 N TYR B 299 SHEET 5 A 5 GLU B 512 GLU B 514 -1 O LYS B 513 N VAL B 505 SHEET 1 B 5 VAL B 341 LEU B 345 0 SHEET 2 B 5 GLN B 328 ASP B 335 -1 N ILE B 333 O ILE B 342 SHEET 3 B 5 TYR B 591 GLY B 598 -1 O GLY B 598 N GLN B 328 SHEET 4 B 5 ASP B 581 THR B 588 -1 N PHE B 584 O VAL B 595 SHEET 5 B 5 GLN B 554 THR B 560 -1 N GLY B 559 O LEU B 583 SHEET 1 C 2 ILE B 393 ASP B 396 0 SHEET 2 C 2 GLY B 417 THR B 420 -1 O ILE B 419 N VAL B 394 SHEET 1 D 2 THR B 495 TYR B 497 0 SHEET 2 D 2 GLY B 519 ARG B 521 -1 O THR B 520 N TYR B 496 SHEET 1 E 2 VAL B 578 ALA B 579 0 SHEET 2 E 2 LEU B 606 VAL B 607 -1 O LEU B 606 N ALA B 579 SHEET 1 F 2 TYR B 641 ASN B 643 0 SHEET 2 F 2 PHE B 646 PHE B 648 -1 O PHE B 646 N ASN B 643 SHEET 1 G 5 LEU C 62 ASP C 65 0 SHEET 2 G 5 LYS C 54 TYR C 56 -1 N ILE C 55 O ILE C 63 SHEET 3 G 5 MET D 296 THR D 300 1 O VAL D 298 N TYR C 56 SHEET 4 G 5 ILE D 502 PHE D 507 -1 O LYS D 504 N TYR D 299 SHEET 5 G 5 GLU D 512 GLU D 514 -1 O LYS D 513 N VAL D 505 SHEET 1 H 5 VAL D 341 LEU D 345 0 SHEET 2 H 5 GLN D 328 ASP D 335 -1 N ILE D 333 O ILE D 342 SHEET 3 H 5 TYR D 591 GLY D 598 -1 O TRP D 596 N ALA D 330 SHEET 4 H 5 GLU D 582 TYR D 587 -1 N PHE D 584 O VAL D 595 SHEET 5 H 5 ALA D 555 THR D 560 -1 N GLY D 559 O LEU D 583 SHEET 1 I 2 ILE D 393 ASP D 396 0 SHEET 2 I 2 GLY D 417 THR D 420 -1 O ILE D 419 N VAL D 394 SHEET 1 J 2 THR D 495 TYR D 496 0 SHEET 2 J 2 THR D 520 ARG D 521 -1 O THR D 520 N TYR D 496 SHEET 1 K 2 VAL D 578 ALA D 579 0 SHEET 2 K 2 LEU D 606 VAL D 607 -1 O LEU D 606 N ALA D 579 SHEET 1 L 2 LEU D 640 ASN D 643 0 SHEET 2 L 2 PHE D 646 LYS D 649 -1 O PHE D 648 N TYR D 641 LINK OG SER B 370 C7 BMG B 701 1555 1555 1.36 LINK OG SER D 370 C7 BMG D 701 1555 1555 1.36 LINK ND1 HIS B 309 ZN ZN B 801 1555 1555 2.06 LINK ND1 HIS B 395 ZN ZN B 802 1555 1555 2.11 LINK OE1 GLU B 435 ZN ZN B 802 1555 1555 1.89 LINK ND1 HIS B 460 ZN ZN B 803 1555 1555 2.04 LINK ND1 HIS D 309 ZN ZN D 805 1555 1555 2.20 LINK OE2 GLU D 318 ZN ZN D 808 1555 1555 2.32 LINK OH TYR D 319 ZN ZN D 808 1555 1555 2.19 LINK ND1 HIS D 395 ZN ZN D 806 1555 1555 2.05 LINK OE2 GLU D 435 ZN ZN D 806 1555 1555 1.80 LINK ND1 HIS D 460 ZN ZN D 807 1555 1555 2.16 SITE 1 AC1 3 HIS B 309 TYR B 319 GLU B 514 SITE 1 AC2 3 HIS B 395 GLU B 397 GLU B 435 SITE 1 AC3 3 HIS B 460 GLU D 566 HIS D 571 SITE 1 AC4 3 GLU B 318 TYR B 319 HIS B 503 SITE 1 AC5 4 HIS D 309 ASP D 312 TYR D 319 GLU D 514 SITE 1 AC6 3 HIS D 395 GLU D 397 GLU D 435 SITE 1 AC7 3 GLU B 566 HIS B 571 HIS D 460 SITE 1 AC8 4 GLU D 318 TYR D 319 LYS D 504 GLU D 512 SITE 1 AC9 10 SER B 370 TRP B 411 SER B 428 ASN B 430 SITE 2 AC9 10 ILE B 465 THR B 543 LYS B 557 THR B 558 SITE 3 AC9 10 GLY B 559 THR B 560 SITE 1 BC1 9 SER D 370 TRP D 411 SER D 428 ASN D 430 SITE 2 BC1 9 THR D 543 LYS D 557 THR D 558 GLY D 559 SITE 3 BC1 9 THR D 560 CRYST1 185.704 50.665 110.784 90.00 90.00 90.00 P 21 21 2 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 0.005385 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019737 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009027 0.00000