HEADER ELECTRON TRANSPORT 18-MAR-98 1A7V TITLE CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C'; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS; SOURCE 3 ORGANISM_TAXID: 1076 KEYWDS ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR N.SHIBATA,S.IBA,S.MISAKI,T.E.MEYER,R.G.BARTSCH,M.A.CUSANOVICH, AUTHOR 2 Y.HIGUCHI,N.YASUOKA REVDAT 4 30-OCT-24 1A7V 1 REMARK REVDAT 3 02-AUG-23 1A7V 1 REMARK LINK REVDAT 2 24-FEB-09 1A7V 1 VERSN REVDAT 1 17-JUN-98 1A7V 0 JRNL AUTH N.SHIBATA,S.IBA,S.MISAKI,T.E.MEYER,R.G.BARTSCH, JRNL AUTH 2 M.A.CUSANOVICH,Y.MORIMOTO,Y.HIGUCHI,N.YASUOKA JRNL TITL BASIS FOR MONOMER STABILIZATION IN RHODOPSEUDOMONAS JRNL TITL 2 PALUSTRIS CYTOCHROME C' DERIVED FROM THE CRYSTAL STRUCTURE. JRNL REF J.MOL.BIOL. V. 284 751 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9826513 JRNL DOI 10.1006/JMBI.1998.2190 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.5 REMARK 3 NUMBER OF REFLECTIONS : 10028 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 SET) : 0.194 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.200 REMARK 3 FREE R VALUE TEST SET COUNT : 926 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 618 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 82 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 : 1842 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 7.00 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) : 1.850 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.170 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.300 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.300 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.700 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.200 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : RESTRAINED REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : 0.10 ; 100.0 REMARK 3 GROUP 1 B-FACTOR (A**2) : 2.0 ; 4.8 REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A7V 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_1000170502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : SI(111) REMARK 200 OPTICS : NULL 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 : 10513 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 89.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 2CCY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 31.50000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.50000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.75000 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: 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: 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 SG CYS A 113 CBB HEM A 150 2.18 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 LYS A 124 -166.85 176.37 REMARK 500 ASP B 64 64.41 39.85 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 150 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 117 NE2 REMARK 620 2 HEM A 150 NA 101.7 REMARK 620 3 HEM A 150 NB 97.7 89.7 REMARK 620 4 HEM A 150 NC 96.9 161.3 89.1 REMARK 620 5 HEM A 150 ND 97.2 88.5 165.0 87.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 150 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 117 NE2 REMARK 620 2 HEM B 150 NA 103.6 REMARK 620 3 HEM B 150 NB 97.6 89.3 REMARK 620 4 HEM B 150 NC 95.3 161.1 87.2 REMARK 620 5 HEM B 150 ND 97.2 90.6 164.8 88.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: HEA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: HEB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 150 DBREF 1A7V A 1 125 UNP P00149 CYCP_RHOPA 1 125 DBREF 1A7V B 1 125 UNP P00149 CYCP_RHOPA 1 125 SEQRES 1 A 125 GLN THR ASP VAL ILE ALA GLN ARG LYS ALA ILE LEU LYS SEQRES 2 A 125 GLN MET GLY GLU ALA THR LYS PRO ILE ALA ALA MET LEU SEQRES 3 A 125 LYS GLY GLU ALA LYS PHE ASP GLN ALA VAL VAL GLN LYS SEQRES 4 A 125 SER LEU ALA ALA ILE ALA ASP ASP SER LYS LYS LEU PRO SEQRES 5 A 125 ALA LEU PHE PRO ALA ASP SER LYS THR GLY GLY ASP THR SEQRES 6 A 125 ALA ALA LEU PRO LYS ILE TRP GLU ASP LYS ALA LYS PHE SEQRES 7 A 125 ASP ASP LEU PHE ALA LYS LEU ALA ALA ALA ALA THR ALA SEQRES 8 A 125 ALA GLN GLY THR ILE LYS ASP GLU ALA SER LEU LYS ALA SEQRES 9 A 125 ASN ILE GLY GLY VAL LEU GLY ASN CYS LYS SER CYS HIS SEQRES 10 A 125 ASP ASP PHE ARG ALA LYS LYS SER SEQRES 1 B 125 GLN THR ASP VAL ILE ALA GLN ARG LYS ALA ILE LEU LYS SEQRES 2 B 125 GLN MET GLY GLU ALA THR LYS PRO ILE ALA ALA MET LEU SEQRES 3 B 125 LYS GLY GLU ALA LYS PHE ASP GLN ALA VAL VAL GLN LYS SEQRES 4 B 125 SER LEU ALA ALA ILE ALA ASP ASP SER LYS LYS LEU PRO SEQRES 5 B 125 ALA LEU PHE PRO ALA ASP SER LYS THR GLY GLY ASP THR SEQRES 6 B 125 ALA ALA LEU PRO LYS ILE TRP GLU ASP LYS ALA LYS PHE SEQRES 7 B 125 ASP ASP LEU PHE ALA LYS LEU ALA ALA ALA ALA THR ALA SEQRES 8 B 125 ALA GLN GLY THR ILE LYS ASP GLU ALA SER LEU LYS ALA SEQRES 9 B 125 ASN ILE GLY GLY VAL LEU GLY ASN CYS LYS SER CYS HIS SEQRES 10 B 125 ASP ASP PHE ARG ALA LYS LYS SER HET HEM A 150 43 HET HEM B 150 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *195(H2 O) HELIX 1 1 VAL A 4 LEU A 26 1 23 HELIX 2 2 GLN A 34 LEU A 54 1 21 HELIX 3 3 PRO A 69 GLU A 73 5 5 HELIX 4 4 LYS A 75 THR A 95 1 21 HELIX 5 5 GLU A 99 PHE A 120 1 22 HELIX 6 6 VAL B 4 LEU B 26 1 23 HELIX 7 7 GLN B 34 ALA B 53 1 20 HELIX 8 9 PRO B 69 GLU B 73 5 5 HELIX 9 10 LYS B 75 THR B 95 1 21 HELIX 10 11 GLU B 99 PHE B 120 1 22 LINK SG CYS A 113 CAB HEM A 150 1555 1555 1.84 LINK SG CYS A 116 CAC HEM A 150 1555 1555 1.82 LINK SG CYS B 113 CAB HEM B 150 1555 1555 1.86 LINK SG CYS B 116 CAC HEM B 150 1555 1555 1.81 LINK NE2 HIS A 117 FE HEM A 150 1555 1555 1.94 LINK NE2 HIS B 117 FE HEM B 150 1555 1555 1.93 SITE 1 HEA 2 HIS A 117 HEM A 150 SITE 1 HEB 2 HIS B 117 HEM B 150 SITE 1 AC1 14 ARG A 8 LYS A 9 LEU A 12 MET A 15 SITE 2 AC1 14 THR A 65 ALA A 66 PHE A 78 LEU A 81 SITE 3 AC1 14 PHE A 82 CYS A 113 CYS A 116 HIS A 117 SITE 4 AC1 14 PHE A 120 HOH A 151 SITE 1 AC2 16 ARG B 8 LYS B 9 LEU B 12 LYS B 13 SITE 2 AC2 16 MET B 15 THR B 65 ALA B 66 PHE B 78 SITE 3 AC2 16 LEU B 81 PHE B 82 CYS B 113 CYS B 116 SITE 4 AC2 16 HIS B 117 PHE B 120 ARG B 121 HOH B 171 CRYST1 63.000 113.500 34.500 90.00 90.00 90.00 P 21 21 21 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 0.015873 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028986 0.00000 MTRIX1 1 -0.997291 0.046599 0.056917 58.06750 1 MTRIX2 1 -0.049179 -0.997784 -0.044807 79.90550 1 MTRIX3 1 0.054703 -0.047485 0.997373 -0.06070 1