HEADER ELECTRON TRANSPORT 09-APR-96 1CPR TITLE ST. LOUIS CYTOCHROME C' FROM THE PURPLE PHOTOTROPIC BACTERIUM, TITLE 2 RHODOBACTER CAPSULATUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C'; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER CAPSULATUS; SOURCE 3 ORGANISM_TAXID: 1061; SOURCE 4 STRAIN: ST. LOUIS KEYWDS ELECTRON TRANSPORT, HEME PROTEIN, CYTOCHROME EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV,S.MISAKI,T.E.MEYER,M.A.CUSANOVICH,N.YASUOKA REVDAT 4 20-NOV-24 1CPR 1 REMARK LINK REVDAT 3 24-FEB-09 1CPR 1 VERSN REVDAT 2 15-FEB-05 1CPR 1 JRNL REVDAT 1 27-JAN-97 1CPR 0 JRNL AUTH T.H.TAHIROV,S.MISAKI,T.E.MEYER,M.A.CUSANOVICH,Y.HIGUCHI, JRNL AUTH 2 N.YASUOKA JRNL TITL STRUCTURE OF CYTOCHROME C' FROM RHODOBACTER CAPSULATUS JRNL TITL 2 STRAIN ST LOUIS: AN UNUSUAL MOLECULAR ASSOCIATION INDUCED BY JRNL TITL 3 BRIDGING ZN IONS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 53 658 1997 JRNL REFN ISSN 0907-4449 JRNL PMID 15299853 JRNL DOI 10.1107/S0907444997005805 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.H.TAHIROV,S.MISAKI,T.E.MEYER,M.A.CUSANOVICH,Y.HIGUCHI, REMARK 1 AUTH 2 N.YASUOKA REMARK 1 TITL HIGH-RESOLUTION CRYSTAL STRUCTURES OF TWO POLYMORPHS OF REMARK 1 TITL 2 CYTOCHROME C' FROM THE PURPLE PHOTOTROPHIC BACTERIUM REMARK 1 TITL 3 RHODOBACTER CAPSULATUS REMARK 1 REF J.MOL.BIOL. V. 259 467 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.H.TAHIROV,S.MISAKI,T.E.MEYER,M.A.CUSANOVICH,Y.HIGUCHI, REMARK 1 AUTH 2 N.YASUOKA REMARK 1 TITL CONCERTED MOVEMENT OF SIDE CHAINS IN THE HAEM VICINITY REMARK 1 TITL 2 OBSERVED ON LIGAND BINDING IN CYTOCHROME C' FROM RHODOBACTER REMARK 1 TITL 3 CAPSULATUS REMARK 1 REF NAT.STRUCT.BIOL. V. 3 459 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 2.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 919 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.340 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.02 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.510 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CPR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172465. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-95 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6988 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 200 DATA REDUNDANCY : 3.880 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 2.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.42500 REMARK 290 SMTRY3 2 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 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 30 64.56 -166.58 REMARK 500 TRP A 75 0.31 -69.86 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 A 133 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 11 OE2 REMARK 620 2 HEM A 136 O2A 100.8 REMARK 620 3 HEM A 136 O1A 112.6 58.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 130 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 32 OD1 REMARK 620 2 GLU A 34 OE1 114.5 REMARK 620 3 ASP A 124 OD2 158.4 79.2 REMARK 620 4 ASP A 124 OD1 103.0 110.5 55.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 135 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 NE2 REMARK 620 2 HOH A 172 O 112.1 REMARK 620 3 HOH A 183 O 91.2 114.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 132 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 122 ND1 REMARK 620 2 HOH A 148 O 97.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 136 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 122 NE2 REMARK 620 2 HEM A 136 NA 100.4 REMARK 620 3 HEM A 136 NB 92.7 87.5 REMARK 620 4 HEM A 136 NC 92.8 166.5 89.2 REMARK 620 5 HEM A 136 ND 97.4 89.3 169.8 91.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 133 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 134 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 136 DBREF 1CPR A 1 129 UNP P00147 CYCP_RHOCA 22 150 SEQRES 1 A 129 ALA ASP THR LYS GLU VAL LEU GLU ALA ARG GLU ALA TYR SEQRES 2 A 129 PHE LYS SER LEU GLY GLY SER MET LYS ALA MET THR GLY SEQRES 3 A 129 VAL ALA LYS ALA PHE ASP ALA GLU ALA ALA LYS VAL GLU SEQRES 4 A 129 ALA ALA LYS LEU GLU LYS ILE LEU ALA THR ASP VAL ALA SEQRES 5 A 129 PRO LEU PHE PRO ALA GLY THR SER SER THR ASP LEU PRO SEQRES 6 A 129 GLY GLN THR GLU ALA LYS ALA ALA ILE TRP ALA ASN MET SEQRES 7 A 129 ASP ASP PHE GLY ALA LYS GLY LYS ALA MET HIS ASP ALA SEQRES 8 A 129 GLY GLY ALA VAL ILE ALA ALA ALA ASN ALA GLY ASP GLY SEQRES 9 A 129 ALA ALA PHE GLY ALA ALA LEU GLN LYS LEU GLY GLY THR SEQRES 10 A 129 CYS LYS ALA CYS HIS ASP ASP TYR ARG GLU GLU ASP HET ZN A 130 1 HET ZN A 131 1 HET ZN A 132 1 HET ZN A 133 1 HET ZN A 134 1 HET ZN A 135 1 HET HEM A 136 43 HETNAM ZN ZINC ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 ZN 6(ZN 2+) FORMUL 8 HEM C34 H32 FE N4 O4 FORMUL 9 HOH *47(H2 O) HELIX 1 1 THR A 3 ALA A 30 1 28 HELIX 2 2 ALA A 33 ALA A 48 1 16 HELIX 3 3 ALA A 52 LEU A 54 5 3 HELIX 4 4 ALA A 72 ALA A 76 5 5 HELIX 5 5 MET A 78 ASN A 100 1 23 HELIX 6 6 GLY A 104 TYR A 125 1 22 LINK SG CYS A 118 CAB HEM A 136 1555 1555 1.77 LINK SG CYS A 121 CAC HEM A 136 1555 1555 1.78 LINK OE2 GLU A 11 ZN ZN A 133 1555 1555 2.06 LINK OD1 ASP A 32 ZN ZN A 130 1555 1555 2.12 LINK OE1 GLU A 34 ZN ZN A 130 1555 1555 2.04 LINK ND1 HIS A 89 ZN ZN A 134 1555 1555 2.14 LINK NE2 HIS A 89 ZN ZN A 135 1555 1555 2.10 LINK ND1 HIS A 122 ZN ZN A 132 1555 1555 2.10 LINK NE2 HIS A 122 FE HEM A 136 1555 1555 1.99 LINK OD2 ASP A 124 ZN ZN A 130 1556 1555 2.61 LINK OD1 ASP A 124 ZN ZN A 130 1556 1555 1.98 LINK ZN ZN A 132 O HOH A 148 1555 1555 2.41 LINK ZN ZN A 133 O2A HEM A 136 1555 1555 2.07 LINK ZN ZN A 133 O1A HEM A 136 1555 1555 2.41 LINK ZN ZN A 135 O HOH A 172 1555 1555 2.62 LINK ZN ZN A 135 O HOH A 183 1555 1555 2.48 SITE 1 AC1 4 ASP A 32 GLU A 34 ASP A 124 ZN A 131 SITE 1 AC2 4 GLU A 34 ASP A 124 ZN A 130 HOH A 137 SITE 1 AC3 2 HIS A 122 HOH A 148 SITE 1 AC4 2 GLU A 11 HEM A 136 SITE 1 AC5 1 HIS A 89 SITE 1 AC6 5 TYR A 13 THR A 49 HIS A 89 HOH A 172 SITE 2 AC6 5 HOH A 183 SITE 1 AC7 17 ARG A 10 GLU A 11 PHE A 14 LYS A 15 SITE 2 AC7 17 LEU A 17 THR A 68 GLU A 69 PHE A 81 SITE 3 AC7 17 GLY A 85 THR A 117 CYS A 118 CYS A 121 SITE 4 AC7 17 HIS A 122 ARG A 126 ZN A 133 HOH A 140 SITE 5 AC7 17 HOH A 179 CRYST1 39.680 46.850 40.750 90.00 110.94 90.00 P 1 21 1 2 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 0.025202 0.000000 0.009644 0.00000 SCALE2 0.000000 0.021345 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026275 0.00000