HEADER ELECTRON TRANSPORT (HEME PROTEIN) 18-MAR-96 1NBB TITLE N-BUTYLISOCYANIDE BOUND RHODOBACTER CAPSULATUS CYTOCHROME C' COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C'; COMPND 3 CHAIN: A, B; COMPND 4 OTHER_DETAILS: N-BUTYLISOCYANIDE BOUND TO HEME IRON SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER CAPSULATUS; SOURCE 3 ORGANISM_TAXID: 1061; SOURCE 4 STRAIN: M110 KEYWDS ELECTRON TRANSPORT, CYTOCHROME, HEME PROTEIN, ELECTRON KEYWDS 2 TRANSPORT (HEME PROTEIN) EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV,S.MISAKI,T.E.MEYER,M.A.CUSANOVICH,Y.HIGUCHI, AUTHOR 2 N.YASUOKA REVDAT 2 24-FEB-09 1NBB 1 VERSN REVDAT 1 17-AUG-96 1NBB 0 JRNL AUTH T.H.TAHIROV,S.MISAKI,T.E.MEYER,M.A.CUSANOVICH, JRNL AUTH 2 Y.HIGUCHI,N.YASUOKA JRNL TITL CONCERTED MOVEMENT OF SIDE CHAINS IN THE HAEM JRNL TITL 2 VICINITY OBSERVED ON LIGAND BINDING IN CYTOCHROME JRNL TITL 3 C' FROM RHODOBACTER CAPSULATUS. JRNL REF NAT.STRUCT.BIOL. V. 3 459 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8612077 JRNL DOI 10.1038/NSB0596-459 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.H.TAHIROV,S.MISAKI,T.E.MEYER,M.A.CUSANOVICH, REMARK 1 AUTH 2 N.YASUOKA REMARK 1 TITL CRYSTAL STRUCTURES OF CYTOCHROME C' FROM REMARK 1 TITL 2 RHODOBACTER CAPSULATUS STRAIN ST. LOUIS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH T.H.TAHIROV,S.MISAKI,T.E.MEYER,M.A.CUSANOVICH, REMARK 1 AUTH 2 Y.HIGUCHI,N.YASUOKA REMARK 1 TITL HIGH-RESOLUTION CRYSTAL STRUCTURES OF TWO REMARK 1 TITL 2 POLYMORPHS OF CYTOCHROME C' FROM THE PURPLE REMARK 1 TITL 3 PHOTOTROPHIC BACTERIUM RHODOBACTER CAPSULATUS REMARK 1 REF J.MOL.BIOL. V. 259 467 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 9841 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) : 0.174 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 : 1845 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 101 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.87 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.62 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.22 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.81 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 1NBB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-95 REMARK 200 TEMPERATURE (KELVIN) : 283 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DOUBLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49034 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 4.440 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.0 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 FOR SHELL : 3.100 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 (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 26.19739 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.26750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.76538 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.19739 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.26750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 44.76538 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 ASP B 2 -143.36 -68.21 REMARK 500 THR B 3 -61.41 -135.48 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 HEM A 130 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 122 NE2 REMARK 620 2 NBN A 131 C 177.6 REMARK 620 3 NBN A 131 N 169.6 8.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 130 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 122 NE2 REMARK 620 2 NBN B 131 C 173.2 REMARK 620 3 NBN B 131 N 169.1 4.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 130 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NBN A 131 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 130 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NBN B 131 DBREF 1NBB A 1 129 UNP P00147 CYCP_RHOCA 22 150 DBREF 1NBB B 1 129 UNP P00147 CYCP_RHOCA 22 150 SEQADV 1NBB GLU A 90 UNP P00147 ASP 111 CONFLICT SEQADV 1NBB GLU B 90 UNP P00147 ASP 111 CONFLICT 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 GLU 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 SEQRES 1 B 129 ALA ASP THR LYS GLU VAL LEU GLU ALA ARG GLU ALA TYR SEQRES 2 B 129 PHE LYS SER LEU GLY GLY SER MET LYS ALA MET THR GLY SEQRES 3 B 129 VAL ALA LYS ALA PHE ASP ALA GLU ALA ALA LYS VAL GLU SEQRES 4 B 129 ALA ALA LYS LEU GLU LYS ILE LEU ALA THR ASP VAL ALA SEQRES 5 B 129 PRO LEU PHE PRO ALA GLY THR SER SER THR ASP LEU PRO SEQRES 6 B 129 GLY GLN THR GLU ALA LYS ALA ALA ILE TRP ALA ASN MET SEQRES 7 B 129 ASP ASP PHE GLY ALA LYS GLY LYS ALA MET HIS GLU ALA SEQRES 8 B 129 GLY GLY ALA VAL ILE ALA ALA ALA ASN ALA GLY ASP GLY SEQRES 9 B 129 ALA ALA PHE GLY ALA ALA LEU GLN LYS LEU GLY GLY THR SEQRES 10 B 129 CYS LYS ALA CYS HIS ASP ASP TYR ARG GLU GLU ASP HET HEM A 130 43 HET NBN A 131 6 HET HEM B 130 43 HET NBN B 131 6 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NBN N-BUTYL ISOCYANIDE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 NBN 2(C5 H9 N) FORMUL 7 HOH *101(H2 O) HELIX 1 1 THR A 3 LYS A 29 1 27 HELIX 2 2 ALA A 33 ILE A 46 1 14 HELIX 3 4 ALA A 73 ALA A 76 5 4 HELIX 4 5 MET A 78 ALA A 101 1 24 HELIX 5 6 GLY A 104 TYR A 125 1 22 HELIX 6 7 THR B 3 LYS B 29 1 27 HELIX 7 8 ALA B 33 ILE B 46 1 14 HELIX 8 10 ALA B 73 ALA B 76 1 4 HELIX 9 11 MET B 78 ALA B 101 1 24 HELIX 10 12 GLY B 104 TYR B 125 1 22 LINK FE HEM A 130 NE2 HIS A 122 1555 1555 1.98 LINK FE HEM A 130 C NBN A 131 1555 1555 1.95 LINK CAB HEM A 130 SG CYS A 118 1555 1555 1.79 LINK CAC HEM A 130 SG CYS A 121 1555 1555 1.79 LINK FE HEM B 130 NE2 HIS B 122 1555 1555 1.95 LINK FE HEM B 130 C NBN B 131 1555 1555 1.90 LINK CAB HEM B 130 SG CYS B 118 1555 1555 1.80 LINK CAC HEM B 130 SG CYS B 121 1555 1555 1.77 LINK FE HEM A 130 N NBN A 131 1555 1555 3.06 LINK FE HEM B 130 N NBN B 131 1555 1555 3.04 SITE 1 AC1 13 ARG A 10 PHE A 14 MET A 21 THR A 68 SITE 2 AC1 13 GLU A 69 PHE A 81 LYS A 84 GLY A 85 SITE 3 AC1 13 CYS A 118 CYS A 121 HIS A 122 ARG A 126 SITE 4 AC1 13 NBN A 131 SITE 1 AC2 3 PHE A 14 VAL A 51 HEM A 130 SITE 1 AC3 19 LYS A 4 ARG B 10 PHE B 14 MET B 21 SITE 2 AC3 19 THR B 68 GLU B 69 PHE B 81 LYS B 84 SITE 3 AC3 19 GLY B 85 THR B 117 CYS B 118 CYS B 121 SITE 4 AC3 19 HIS B 122 TYR B 125 ARG B 126 GLU B 128 SITE 5 AC3 19 NBN B 131 HOH B 149 HOH B 172 SITE 1 AC4 3 PHE B 14 VAL B 51 HEM B 130 CRYST1 47.734 70.535 89.652 90.00 87.02 90.00 I 1 2 1 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 0.020949 0.000000 -0.001091 0.00000 SCALE2 0.000000 0.014177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011169 0.00000