HEADER OXIDOREDUCTASE 20-MAR-10 2X9I TITLE STRUCTURE OF THE MUTANT D105N OF PHYCOERYTHROBILIN SYNTHASE PEBS FROM TITLE 2 THE CYANOPHAGE P-SSM2 IN COMPLEX WITH BOUND SUBSTRATE BILIVERDIN IXA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYCOBILIN SYNTHASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: (3Z)-PHYCOERYTHROBILIN \: FERREDOXIN OXIDOREDUCTASE, COMPND 5 BILIVERDIN REDUCTASE; COMPND 6 EC: 1.3.7.6; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROCHLOROCOCCUS PHAGE P-SSM2; SOURCE 3 ORGANISM_TAXID: 268746; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-3; SOURCE 8 OTHER_DETAILS: CYANOPHAGE KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.W.U.BUSCH,N.FRANKENBERG-DINKEL,E.HOFMANN REVDAT 3 20-DEC-23 2X9I 1 REMARK REVDAT 2 25-MAY-11 2X9I 1 JRNL REVDAT 1 17-NOV-10 2X9I 0 JRNL AUTH A.W.U.BUSCH,E.J.REIJERSE,W.LUBITZ,E.HOFMANN, JRNL AUTH 2 N.FRANKENBERG-DINKEL JRNL TITL RADICAL MECHANISM OF CYANOPHAGE PHYCOERYTHROBILIN SYNTHASE JRNL TITL 2 (PEBS). JRNL REF BIOCHEM.J. V. 433 469 2011 JRNL REFN ISSN 0264-6021 JRNL PMID 21050180 JRNL DOI 10.1042/BJ20101642 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 50817 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2561 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.0178 - 5.7610 0.97 2681 166 0.1583 0.1791 REMARK 3 2 5.7610 - 4.5743 0.98 2727 121 0.1304 0.1746 REMARK 3 3 4.5743 - 3.9966 0.97 2657 175 0.1296 0.1495 REMARK 3 4 3.9966 - 3.6314 0.96 2676 133 0.1492 0.1665 REMARK 3 5 3.6314 - 3.3712 0.97 2660 146 0.1733 0.1828 REMARK 3 6 3.3712 - 3.1725 0.97 2672 144 0.1933 0.2674 REMARK 3 7 3.1725 - 3.0137 0.96 2643 168 0.2048 0.2596 REMARK 3 8 3.0137 - 2.8825 0.97 2629 195 0.2074 0.2471 REMARK 3 9 2.8825 - 2.7716 0.97 2623 204 0.1926 0.2346 REMARK 3 10 2.7716 - 2.6759 0.97 2840 0 0.1897 0.0000 REMARK 3 11 2.6759 - 2.5923 0.97 2618 215 0.1872 0.2218 REMARK 3 12 2.5923 - 2.5182 0.97 2537 284 0.1859 0.2572 REMARK 3 13 2.5182 - 2.4519 0.97 2828 0 0.1866 0.0000 REMARK 3 14 2.4519 - 2.3921 0.97 2492 299 0.1843 0.2329 REMARK 3 15 2.3921 - 2.3377 0.97 2858 0 0.1875 0.0000 REMARK 3 16 2.3377 - 2.2880 0.97 2528 311 0.1976 0.2578 REMARK 3 17 2.2880 - 2.2422 0.97 2826 0 0.2029 0.0000 REMARK 3 18 2.2422 - 2.1999 0.96 2761 0 0.2096 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 30.74 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.57890 REMARK 3 B22 (A**2) : 14.11410 REMARK 3 B33 (A**2) : -7.53530 REMARK 3 B12 (A**2) : -0.85860 REMARK 3 B13 (A**2) : 0.97260 REMARK 3 B23 (A**2) : 7.38640 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 7250 REMARK 3 ANGLE : 1.435 9808 REMARK 3 CHIRALITY : 0.096 974 REMARK 3 PLANARITY : 0.007 1258 REMARK 3 DIHEDRAL : 18.106 2598 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 7 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 22:135 OR RESSEQ REMARK 3 148:202 OR RESSEQ 209:233 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 22:135 OR RESSEQ REMARK 3 148:202 OR RESSEQ 209:233 ) REMARK 3 ATOM PAIRS NUMBER : 1575 REMARK 3 RMSD : 0.008 REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 22:135 OR RESSEQ REMARK 3 148:202 OR RESSEQ 209:233 ) REMARK 3 SELECTION : CHAIN C AND (RESSEQ 22:135 OR RESSEQ REMARK 3 148:202 OR RESSEQ 209:233 ) REMARK 3 ATOM PAIRS NUMBER : 1575 REMARK 3 RMSD : 0.008 REMARK 3 NCS OPERATOR : 3 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 22:135 OR RESSEQ REMARK 3 148:202 OR RESSEQ 209:233 ) REMARK 3 SELECTION : CHAIN D AND (RESSEQ 22:135 OR RESSEQ REMARK 3 148:202 OR RESSEQ 209:233 ) REMARK 3 ATOM PAIRS NUMBER : 1575 REMARK 3 RMSD : 0.007 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 21 OR RESSEQ 136:147 REMARK 3 OR RESSEQ 203:208) AND BACKBONE REMARK 3 SELECTION : CHAIN D AND (RESSEQ 21 OR RESSEQ 136:147 REMARK 3 OR RESSEQ 203:208) AND BACKBONE REMARK 3 ATOM PAIRS NUMBER : 76 REMARK 3 RMSD : 0.004 REMARK 3 NCS GROUP : 3 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 21 OR RESSEQ 136:147 REMARK 3 OR RESSEQ 203:208) AND SIDECHAIN REMARK 3 SELECTION : CHAIN D AND (RESSEQ 21 OR RESSEQ 136:147 REMARK 3 OR RESSEQ 203:208) AND SIDECHAIN REMARK 3 ATOM PAIRS NUMBER : 83 REMARK 3 RMSD : 0.460 REMARK 3 NCS GROUP : 4 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B AND (RESSEQ 21 OR RESSEQ 136:147 REMARK 3 OR RESSEQ 203:208) AND BACKBONE REMARK 3 SELECTION : CHAIN C AND (RESSEQ 21 OR RESSEQ 136:147 REMARK 3 OR RESSEQ 203:208) AND BACKBONE REMARK 3 ATOM PAIRS NUMBER : 60 REMARK 3 RMSD : 0.004 REMARK 3 NCS GROUP : 5 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B AND (RESSEQ 21 OR RESSEQ 136:147 REMARK 3 OR RESSEQ 203:208) AND SIDECHAIN REMARK 3 SELECTION : CHAIN C AND (RESSEQ 21 OR RESSEQ 136:147 REMARK 3 OR RESSEQ 203:208) AND SIDECHAIN REMARK 3 ATOM PAIRS NUMBER : 66 REMARK 3 RMSD : 0.679 REMARK 3 NCS GROUP : 6 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 1234) REMARK 3 SELECTION : CHAIN D AND (RESSEQ 1234) REMARK 3 ATOM PAIRS NUMBER : 43 REMARK 3 RMSD : 0.003 REMARK 3 NCS GROUP : 7 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B AND (RESSEQ 1234) REMARK 3 SELECTION : CHAIN C AND (RESSEQ 1234) REMARK 3 ATOM PAIRS NUMBER : 43 REMARK 3 RMSD : 0.003 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2X9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1290043359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50826 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 43.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.730 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2VGR REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 170MM (NH4)2SO4, 20%PEG3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 105 TO ASN REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASP 105 TO ASN REMARK 400 ENGINEERED RESIDUE IN CHAIN C, ASP 105 TO ASN REMARK 400 ENGINEERED RESIDUE IN CHAIN D, ASP 105 TO ASN 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 THR A 2 REMARK 465 LYS A 3 REMARK 465 ASN A 4 REMARK 465 PRO A 5 REMARK 465 ARG A 6 REMARK 465 ASN A 7 REMARK 465 ASN A 8 REMARK 465 LYS A 9 REMARK 465 PRO A 10 REMARK 465 LYS A 11 REMARK 465 LYS A 12 REMARK 465 ILE A 13 REMARK 465 LEU A 14 REMARK 465 ASP A 15 REMARK 465 SER A 16 REMARK 465 SER A 17 REMARK 465 TYR A 18 REMARK 465 LYS A 19 REMARK 465 SER A 20 REMARK 465 THR A 53 REMARK 465 LYS A 54 REMARK 465 ASP A 55 REMARK 465 GLY A 56 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 LYS B 3 REMARK 465 ASN B 4 REMARK 465 PRO B 5 REMARK 465 ARG B 6 REMARK 465 ASN B 7 REMARK 465 ASN B 8 REMARK 465 LYS B 9 REMARK 465 PRO B 10 REMARK 465 LYS B 11 REMARK 465 LYS B 12 REMARK 465 ILE B 13 REMARK 465 LEU B 14 REMARK 465 ASP B 15 REMARK 465 SER B 16 REMARK 465 SER B 17 REMARK 465 TYR B 18 REMARK 465 LYS B 19 REMARK 465 SER B 20 REMARK 465 THR B 53 REMARK 465 LYS B 54 REMARK 465 ASP B 55 REMARK 465 GLY B 56 REMARK 465 ASP B 138 REMARK 465 GLY B 139 REMARK 465 LYS B 140 REMARK 465 TYR B 141 REMARK 465 MET C 1 REMARK 465 THR C 2 REMARK 465 LYS C 3 REMARK 465 ASN C 4 REMARK 465 PRO C 5 REMARK 465 ARG C 6 REMARK 465 ASN C 7 REMARK 465 ASN C 8 REMARK 465 LYS C 9 REMARK 465 PRO C 10 REMARK 465 LYS C 11 REMARK 465 LYS C 12 REMARK 465 ILE C 13 REMARK 465 LEU C 14 REMARK 465 ASP C 15 REMARK 465 SER C 16 REMARK 465 SER C 17 REMARK 465 TYR C 18 REMARK 465 LYS C 19 REMARK 465 SER C 20 REMARK 465 THR C 53 REMARK 465 LYS C 54 REMARK 465 ASP C 55 REMARK 465 GLY C 56 REMARK 465 ASP C 138 REMARK 465 GLY C 139 REMARK 465 LYS C 140 REMARK 465 TYR C 141 REMARK 465 MET D 1 REMARK 465 THR D 2 REMARK 465 LYS D 3 REMARK 465 ASN D 4 REMARK 465 PRO D 5 REMARK 465 ARG D 6 REMARK 465 ASN D 7 REMARK 465 ASN D 8 REMARK 465 LYS D 9 REMARK 465 PRO D 10 REMARK 465 LYS D 11 REMARK 465 LYS D 12 REMARK 465 ILE D 13 REMARK 465 LEU D 14 REMARK 465 ASP D 15 REMARK 465 SER D 16 REMARK 465 SER D 17 REMARK 465 TYR D 18 REMARK 465 LYS D 19 REMARK 465 SER D 20 REMARK 465 THR D 53 REMARK 465 LYS D 54 REMARK 465 ASP D 55 REMARK 465 GLY D 56 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 207 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 PRO D 207 C - N - CA ANGL. DEV. = 9.5 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 HIS A 70 -4.32 77.92 REMARK 500 PHE A 143 -44.29 59.77 REMARK 500 PRO A 207 23.31 -75.55 REMARK 500 HIS B 70 -3.57 77.01 REMARK 500 PHE B 144 162.14 145.13 REMARK 500 LEU B 205 -86.35 -85.29 REMARK 500 PRO B 207 39.71 -74.20 REMARK 500 HIS C 70 -3.94 77.72 REMARK 500 PHE C 144 162.34 145.05 REMARK 500 LEU C 205 -86.21 -85.36 REMARK 500 PRO C 207 39.53 -74.31 REMARK 500 HIS D 70 -3.90 77.67 REMARK 500 PHE D 143 -44.01 59.55 REMARK 500 PRO D 207 23.01 -75.31 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 SO4 A 1235 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1235 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLA C 1234 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLA D 1234 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLA B 1234 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLA A 1234 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VCL RELATED DB: PDB REMARK 900 STRUCTURE OF THE PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE REMARK 900 CYANOPHAGE P-SSM2 IN THE SUBSTRATE FREE FORM REMARK 900 RELATED ID: 2VCK RELATED DB: PDB REMARK 900 STRUCTURE OF THE PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE REMARK 900 CYANOPHAGE P-SSM2 IN COMPLEX WITH THE BOUND SUBSTRATE BILIVERDIN IXA REMARK 900 RELATED ID: 2VGR RELATED DB: PDB REMARK 900 STRUCTURE OF THE WT-PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE REMARK 900 CYANOPHAGE P-SSM2 IN COMPLEX WITH THE BOUND SUBSTRATE BILIVERDIN IXA REMARK 900 RELATED ID: 2X9J RELATED DB: PDB REMARK 900 STRUCTURE OF THE MUTANT D206N OF PHYCOERYTHROBILIN SYNTHASE PEBS REMARK 900 FROM THE CYANOPHAGE P-SSM2 IN COMPLEX WITH BOUND SUBSTRATE REMARK 900 BILIVERDIN IXA DBREF 2X9I A 1 233 UNP Q58MU6 PEBS_BPPRM 1 233 DBREF 2X9I B 1 233 UNP Q58MU6 PEBS_BPPRM 1 233 DBREF 2X9I C 1 233 UNP Q58MU6 PEBS_BPPRM 1 233 DBREF 2X9I D 1 233 UNP Q58MU6 PEBS_BPPRM 1 233 SEQADV 2X9I ASN A 105 UNP Q58MU6 ASP 105 ENGINEERED MUTATION SEQADV 2X9I ASN B 105 UNP Q58MU6 ASP 105 ENGINEERED MUTATION SEQADV 2X9I ASN C 105 UNP Q58MU6 ASP 105 ENGINEERED MUTATION SEQADV 2X9I ASN D 105 UNP Q58MU6 ASP 105 ENGINEERED MUTATION SEQRES 1 A 233 MET THR LYS ASN PRO ARG ASN ASN LYS PRO LYS LYS ILE SEQRES 2 A 233 LEU ASP SER SER TYR LYS SER LYS THR ILE TRP GLN ASN SEQRES 3 A 233 TYR ILE ASP ALA LEU PHE GLU THR PHE PRO GLN LEU GLU SEQRES 4 A 233 ILE SER GLU VAL TRP ALA LYS TRP ASP GLY GLY ASN VAL SEQRES 5 A 233 THR LYS ASP GLY GLY ASP ALA LYS LEU THR ALA ASN ILE SEQRES 6 A 233 ARG THR GLY GLU HIS PHE LEU LYS ALA ARG GLU ALA HIS SEQRES 7 A 233 ILE VAL ASP PRO ASN SER ASP ILE TYR ASN THR ILE LEU SEQRES 8 A 233 TYR PRO LYS THR GLY ALA ASP LEU PRO CYS PHE GLY MET SEQRES 9 A 233 ASN LEU MET LYS PHE SER ASP LYS LYS VAL ILE ILE VAL SEQRES 10 A 233 PHE ASP PHE GLN HIS PRO ARG GLU LYS TYR LEU PHE SER SEQRES 11 A 233 VAL ASP GLY LEU PRO GLU ASP ASP GLY LYS TYR ARG PHE SEQRES 12 A 233 PHE GLU MET GLY ASN HIS PHE SER LYS ASN ILE PHE VAL SEQRES 13 A 233 ARG TYR CYS LYS PRO ASP GLU VAL ASP GLN TYR LEU ASP SEQRES 14 A 233 THR PHE LYS LEU TYR LEU THR LYS TYR LYS GLU MET ILE SEQRES 15 A 233 ASP ASN ASN LYS PRO VAL GLY GLU ASP THR THR VAL TYR SEQRES 16 A 233 SER ASP PHE ASP THR TYR MET THR GLU LEU ASP PRO VAL SEQRES 17 A 233 ARG GLY TYR MET LYS ASN LYS PHE GLY GLU GLY ARG SER SEQRES 18 A 233 GLU ALA PHE VAL ASN ASP PHE LEU PHE SER TYR LYS SEQRES 1 B 233 MET THR LYS ASN PRO ARG ASN ASN LYS PRO LYS LYS ILE SEQRES 2 B 233 LEU ASP SER SER TYR LYS SER LYS THR ILE TRP GLN ASN SEQRES 3 B 233 TYR ILE ASP ALA LEU PHE GLU THR PHE PRO GLN LEU GLU SEQRES 4 B 233 ILE SER GLU VAL TRP ALA LYS TRP ASP GLY GLY ASN VAL SEQRES 5 B 233 THR LYS ASP GLY GLY ASP ALA LYS LEU THR ALA ASN ILE SEQRES 6 B 233 ARG THR GLY GLU HIS PHE LEU LYS ALA ARG GLU ALA HIS SEQRES 7 B 233 ILE VAL ASP PRO ASN SER ASP ILE TYR ASN THR ILE LEU SEQRES 8 B 233 TYR PRO LYS THR GLY ALA ASP LEU PRO CYS PHE GLY MET SEQRES 9 B 233 ASN LEU MET LYS PHE SER ASP LYS LYS VAL ILE ILE VAL SEQRES 10 B 233 PHE ASP PHE GLN HIS PRO ARG GLU LYS TYR LEU PHE SER SEQRES 11 B 233 VAL ASP GLY LEU PRO GLU ASP ASP GLY LYS TYR ARG PHE SEQRES 12 B 233 PHE GLU MET GLY ASN HIS PHE SER LYS ASN ILE PHE VAL SEQRES 13 B 233 ARG TYR CYS LYS PRO ASP GLU VAL ASP GLN TYR LEU ASP SEQRES 14 B 233 THR PHE LYS LEU TYR LEU THR LYS TYR LYS GLU MET ILE SEQRES 15 B 233 ASP ASN ASN LYS PRO VAL GLY GLU ASP THR THR VAL TYR SEQRES 16 B 233 SER ASP PHE ASP THR TYR MET THR GLU LEU ASP PRO VAL SEQRES 17 B 233 ARG GLY TYR MET LYS ASN LYS PHE GLY GLU GLY ARG SER SEQRES 18 B 233 GLU ALA PHE VAL ASN ASP PHE LEU PHE SER TYR LYS SEQRES 1 C 233 MET THR LYS ASN PRO ARG ASN ASN LYS PRO LYS LYS ILE SEQRES 2 C 233 LEU ASP SER SER TYR LYS SER LYS THR ILE TRP GLN ASN SEQRES 3 C 233 TYR ILE ASP ALA LEU PHE GLU THR PHE PRO GLN LEU GLU SEQRES 4 C 233 ILE SER GLU VAL TRP ALA LYS TRP ASP GLY GLY ASN VAL SEQRES 5 C 233 THR LYS ASP GLY GLY ASP ALA LYS LEU THR ALA ASN ILE SEQRES 6 C 233 ARG THR GLY GLU HIS PHE LEU LYS ALA ARG GLU ALA HIS SEQRES 7 C 233 ILE VAL ASP PRO ASN SER ASP ILE TYR ASN THR ILE LEU SEQRES 8 C 233 TYR PRO LYS THR GLY ALA ASP LEU PRO CYS PHE GLY MET SEQRES 9 C 233 ASN LEU MET LYS PHE SER ASP LYS LYS VAL ILE ILE VAL SEQRES 10 C 233 PHE ASP PHE GLN HIS PRO ARG GLU LYS TYR LEU PHE SER SEQRES 11 C 233 VAL ASP GLY LEU PRO GLU ASP ASP GLY LYS TYR ARG PHE SEQRES 12 C 233 PHE GLU MET GLY ASN HIS PHE SER LYS ASN ILE PHE VAL SEQRES 13 C 233 ARG TYR CYS LYS PRO ASP GLU VAL ASP GLN TYR LEU ASP SEQRES 14 C 233 THR PHE LYS LEU TYR LEU THR LYS TYR LYS GLU MET ILE SEQRES 15 C 233 ASP ASN ASN LYS PRO VAL GLY GLU ASP THR THR VAL TYR SEQRES 16 C 233 SER ASP PHE ASP THR TYR MET THR GLU LEU ASP PRO VAL SEQRES 17 C 233 ARG GLY TYR MET LYS ASN LYS PHE GLY GLU GLY ARG SER SEQRES 18 C 233 GLU ALA PHE VAL ASN ASP PHE LEU PHE SER TYR LYS SEQRES 1 D 233 MET THR LYS ASN PRO ARG ASN ASN LYS PRO LYS LYS ILE SEQRES 2 D 233 LEU ASP SER SER TYR LYS SER LYS THR ILE TRP GLN ASN SEQRES 3 D 233 TYR ILE ASP ALA LEU PHE GLU THR PHE PRO GLN LEU GLU SEQRES 4 D 233 ILE SER GLU VAL TRP ALA LYS TRP ASP GLY GLY ASN VAL SEQRES 5 D 233 THR LYS ASP GLY GLY ASP ALA LYS LEU THR ALA ASN ILE SEQRES 6 D 233 ARG THR GLY GLU HIS PHE LEU LYS ALA ARG GLU ALA HIS SEQRES 7 D 233 ILE VAL ASP PRO ASN SER ASP ILE TYR ASN THR ILE LEU SEQRES 8 D 233 TYR PRO LYS THR GLY ALA ASP LEU PRO CYS PHE GLY MET SEQRES 9 D 233 ASN LEU MET LYS PHE SER ASP LYS LYS VAL ILE ILE VAL SEQRES 10 D 233 PHE ASP PHE GLN HIS PRO ARG GLU LYS TYR LEU PHE SER SEQRES 11 D 233 VAL ASP GLY LEU PRO GLU ASP ASP GLY LYS TYR ARG PHE SEQRES 12 D 233 PHE GLU MET GLY ASN HIS PHE SER LYS ASN ILE PHE VAL SEQRES 13 D 233 ARG TYR CYS LYS PRO ASP GLU VAL ASP GLN TYR LEU ASP SEQRES 14 D 233 THR PHE LYS LEU TYR LEU THR LYS TYR LYS GLU MET ILE SEQRES 15 D 233 ASP ASN ASN LYS PRO VAL GLY GLU ASP THR THR VAL TYR SEQRES 16 D 233 SER ASP PHE ASP THR TYR MET THR GLU LEU ASP PRO VAL SEQRES 17 D 233 ARG GLY TYR MET LYS ASN LYS PHE GLY GLU GLY ARG SER SEQRES 18 D 233 GLU ALA PHE VAL ASN ASP PHE LEU PHE SER TYR LYS HET BLA A1234 43 HET SO4 A1235 5 HET BLA B1234 43 HET SO4 B1235 5 HET BLA C1234 43 HET BLA D1234 43 HETNAM BLA BILIVERDINE IX ALPHA HETNAM SO4 SULFATE ION FORMUL 5 BLA 4(C33 H34 N4 O6) FORMUL 6 SO4 2(O4 S 2-) FORMUL 11 HOH *349(H2 O) HELIX 1 1 TRP A 24 PHE A 35 1 12 HELIX 2 2 LYS A 160 GLN A 166 5 7 HELIX 3 3 TYR A 167 LYS A 186 1 20 HELIX 4 4 ASP A 191 VAL A 194 5 4 HELIX 5 5 TYR A 195 ASP A 206 1 12 HELIX 6 6 PRO A 207 GLY A 217 1 11 HELIX 7 7 GLY A 217 PHE A 228 1 12 HELIX 8 8 TRP B 24 PHE B 35 1 12 HELIX 9 9 LYS B 160 GLN B 166 5 7 HELIX 10 10 TYR B 167 LYS B 186 1 20 HELIX 11 11 ASP B 191 VAL B 194 5 4 HELIX 12 12 TYR B 195 GLU B 204 1 10 HELIX 13 13 PRO B 207 GLY B 217 1 11 HELIX 14 14 GLY B 217 PHE B 228 1 12 HELIX 15 15 TRP C 24 PHE C 35 1 12 HELIX 16 16 LYS C 160 GLN C 166 5 7 HELIX 17 17 TYR C 167 LYS C 186 1 20 HELIX 18 18 ASP C 191 VAL C 194 5 4 HELIX 19 19 TYR C 195 GLU C 204 1 10 HELIX 20 20 PRO C 207 GLY C 217 1 11 HELIX 21 21 GLY C 217 PHE C 228 1 12 HELIX 22 22 TRP D 24 PHE D 35 1 12 HELIX 23 23 LYS D 160 GLN D 166 5 7 HELIX 24 24 TYR D 167 LYS D 186 1 20 HELIX 25 25 ASP D 191 VAL D 194 5 4 HELIX 26 26 TYR D 195 ASP D 206 1 12 HELIX 27 27 PRO D 207 GLY D 217 1 11 HELIX 28 28 GLY D 217 PHE D 228 1 12 SHEET 1 AA 7 GLU A 39 GLY A 49 0 SHEET 2 AA 7 ALA A 59 GLY A 68 -1 O ALA A 59 N GLY A 49 SHEET 3 AA 7 PHE A 71 VAL A 80 -1 O PHE A 71 N GLY A 68 SHEET 4 AA 7 ASP A 85 PRO A 93 -1 O ILE A 86 N ILE A 79 SHEET 5 AA 7 CYS A 101 LYS A 108 -1 O PHE A 102 N LEU A 91 SHEET 6 AA 7 VAL A 114 GLN A 121 -1 O ILE A 115 N MET A 107 SHEET 7 AA 7 PHE A 155 CYS A 159 -1 O PHE A 155 N PHE A 118 SHEET 1 BA 7 GLU B 39 GLY B 49 0 SHEET 2 BA 7 ALA B 59 GLY B 68 -1 O ALA B 59 N GLY B 49 SHEET 3 BA 7 PHE B 71 VAL B 80 -1 O PHE B 71 N GLY B 68 SHEET 4 BA 7 ASP B 85 PRO B 93 -1 O ILE B 86 N ILE B 79 SHEET 5 BA 7 CYS B 101 LYS B 108 -1 O PHE B 102 N LEU B 91 SHEET 6 BA 7 VAL B 114 GLN B 121 -1 O ILE B 115 N MET B 107 SHEET 7 BA 7 PHE B 155 CYS B 159 -1 O PHE B 155 N PHE B 118 SHEET 1 CA 7 GLU C 39 GLY C 49 0 SHEET 2 CA 7 ALA C 59 GLY C 68 -1 O ALA C 59 N GLY C 49 SHEET 3 CA 7 PHE C 71 VAL C 80 -1 O PHE C 71 N GLY C 68 SHEET 4 CA 7 ASP C 85 PRO C 93 -1 O ILE C 86 N ILE C 79 SHEET 5 CA 7 CYS C 101 LYS C 108 -1 O PHE C 102 N LEU C 91 SHEET 6 CA 7 VAL C 114 GLN C 121 -1 O ILE C 115 N MET C 107 SHEET 7 CA 7 PHE C 155 CYS C 159 -1 O PHE C 155 N PHE C 118 SHEET 1 DA 7 GLU D 39 GLY D 49 0 SHEET 2 DA 7 ALA D 59 GLY D 68 -1 O ALA D 59 N GLY D 49 SHEET 3 DA 7 PHE D 71 VAL D 80 -1 O PHE D 71 N GLY D 68 SHEET 4 DA 7 ASP D 85 PRO D 93 -1 O ILE D 86 N ILE D 79 SHEET 5 DA 7 CYS D 101 LYS D 108 -1 O PHE D 102 N LEU D 91 SHEET 6 DA 7 VAL D 114 GLN D 121 -1 O ILE D 115 N MET D 107 SHEET 7 DA 7 PHE D 155 CYS D 159 -1 O PHE D 155 N PHE D 118 SITE 1 AC1 4 ASP A 48 ARG A 220 ASP C 48 ARG C 220 SITE 1 AC2 4 ASP B 48 ARG B 220 ASP D 48 ARG D 220 SITE 1 AC3 20 ARG B 142 PHE B 143 ILE C 79 ASN C 88 SITE 2 AC3 20 ILE C 90 GLY C 103 MET C 104 ASN C 105 SITE 3 AC3 20 MET C 107 ILE C 115 GLN C 121 ARG C 142 SITE 4 AC3 20 PHE C 143 PHE C 144 TYR C 158 MET C 202 SITE 5 AC3 20 ASP C 206 PRO C 207 VAL C 208 TYR C 211 SITE 1 AC4 18 ILE D 79 ASN D 88 GLY D 103 MET D 104 SITE 2 AC4 18 ASN D 105 MET D 107 LYS D 113 ILE D 115 SITE 3 AC4 18 GLN D 121 TYR D 141 ARG D 142 PHE D 143 SITE 4 AC4 18 PHE D 144 TYR D 158 MET D 202 ASP D 206 SITE 5 AC4 18 VAL D 208 TYR D 211 SITE 1 AC5 21 ILE B 79 ASN B 88 ILE B 90 GLY B 103 SITE 2 AC5 21 MET B 104 ASN B 105 MET B 107 ILE B 115 SITE 3 AC5 21 GLN B 121 ARG B 142 PHE B 143 PHE B 144 SITE 4 AC5 21 TYR B 158 MET B 202 ASP B 206 PRO B 207 SITE 5 AC5 21 VAL B 208 TYR B 211 HOH B2091 ARG C 142 SITE 6 AC5 21 PHE C 143 SITE 1 AC6 21 ILE A 79 ASN A 88 ILE A 90 GLY A 103 SITE 2 AC6 21 MET A 104 ASN A 105 MET A 107 LYS A 113 SITE 3 AC6 21 ILE A 115 GLN A 121 TYR A 141 ARG A 142 SITE 4 AC6 21 PHE A 143 PHE A 144 TYR A 158 MET A 202 SITE 5 AC6 21 ASP A 206 PRO A 207 VAL A 208 TYR A 211 SITE 6 AC6 21 HOH A2098 CRYST1 52.920 70.140 81.970 109.38 109.25 92.56 P 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 0.018896 0.000845 0.007429 0.00000 SCALE2 0.000000 0.014271 0.005638 0.00000 SCALE3 0.000000 0.000000 0.013894 0.00000 MTRIX1 1 -0.990048 0.134020 0.042945 2.17905 1 MTRIX2 1 -0.129498 -0.748089 -0.650841 45.66210 1 MTRIX3 1 -0.055099 -0.649925 0.757999 -24.81120 1 MTRIX1 2 -0.990168 -0.129089 -0.053876 33.54510 1 MTRIX2 2 -0.133448 0.756307 0.640462 39.13490 1 MTRIX3 2 -0.041930 0.641355 -0.766098 -100.35600 1 MTRIX1 3 0.999976 -0.001900 0.006642 -25.96230 1 MTRIX2 3 -0.001917 -0.999995 0.002639 57.77260 1 MTRIX3 3 0.006637 -0.002652 -0.999974 -52.13340 1