HEADER ELECTRON TRANSPORT 31-MAR-08 3CP5 TITLE CYTOCHROME C FROM RHODOTHERMUS MARINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-152; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOTHERMUS MARINUS; SOURCE 3 ORGANISM_COMMON: RHODOTHERMUS OBAMENSIS; SOURCE 4 ORGANISM_TAXID: 29549; SOURCE 5 GENE: CYTC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYTOCHROME C, ELECTRON TRANSFER PROTEIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.STELTER,A.MELO,L.SARAIVA,M.TEIXEIRA,M.ARCHER REVDAT 5 30-OCT-24 3CP5 1 REMARK LINK REVDAT 4 24-FEB-09 3CP5 1 VERSN REVDAT 3 25-NOV-08 3CP5 1 JRNL REVDAT 2 11-NOV-08 3CP5 1 DBREF REVDAT 1 28-OCT-08 3CP5 0 JRNL AUTH M.STELTER,A.M.MELO,M.M.PEREIRA,C.M.GOMES,G.O.HREGGVIDSSON, JRNL AUTH 2 S.HJORLEIFSDOTTIR,L.M.SARAIVA,M.TEIXEIRA,M.ARCHER JRNL TITL A NOVEL TYPE OF MONOHEME CYTOCHROME C: BIOCHEMICAL AND JRNL TITL 2 STRUCTURAL CHARACTERIZATION AT 1.23 A RESOLUTION OF JRNL TITL 3 RHODOTHERMUS MARINUS CYTOCHROME C JRNL REF BIOCHEMISTRY V. 47 11953 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18855424 JRNL DOI 10.1021/BI800999G REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.130 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.130 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1489 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 29669 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.108 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.107 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1136 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21492 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 912 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1094.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 885.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 9 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10515 REMARK 3 NUMBER OF RESTRAINTS : 12788 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.010 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.074 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.083 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.029 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.064 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.090 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: RESTRAINTS ON PROSTHETIC GROUPS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CP5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047045. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 2.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29745 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 42.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG8K, 0.2M AMMONIUM SULFATE, 8% REMARK 280 HEXANEDIOL, 50MM SODIUM CITRATE, PH2.2, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 16.32200 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 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 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 THR A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 GLN A 8 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 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 62 CB - CG - OD1 ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG A 66 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 118 NE - CZ - NH1 ANGL. DEV. = 4.0 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 PHE A 55 -120.07 -142.25 REMARK 500 ASN A 78 54.97 -144.49 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 HEC A 202 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 49 NE2 REMARK 620 2 HEC A 202 NA 88.8 REMARK 620 3 HEC A 202 NB 88.3 91.8 REMARK 620 4 HEC A 202 NC 89.9 178.6 88.5 REMARK 620 5 HEC A 202 ND 87.8 88.5 176.1 91.1 REMARK 620 6 MET A 100 SD 175.6 87.9 94.7 93.4 89.2 REMARK 620 N 1 2 3 4 5 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 202 DBREF 3CP5 A 1 124 UNP B3FQS5 B3FQS5_RHOMR 29 152 SEQRES 1 A 124 THR GLU SER GLY THR ALA ALA GLN ASP PRO GLU ALA LEU SEQRES 2 A 124 ALA ALA GLU ILE GLY PRO VAL LYS GLN VAL SER LEU GLY SEQRES 3 A 124 GLU GLN ILE ASP ALA ALA LEU ALA GLN GLN GLY GLU GLN SEQRES 4 A 124 LEU PHE ASN THR TYR CYS THR ALA CYS HIS ARG LEU ASP SEQRES 5 A 124 GLU ARG PHE ILE GLY PRO ALA LEU ARG ASP VAL THR LYS SEQRES 6 A 124 ARG ARG GLY PRO VAL TYR ILE MET ASN VAL MET LEU ASN SEQRES 7 A 124 PRO ASN GLY MET ILE GLN ARG HIS PRO VAL MET LYS GLN SEQRES 8 A 124 LEU VAL GLN GLU TYR GLY THR MET MET THR ASP MET ALA SEQRES 9 A 124 LEU SER GLU GLU GLN ALA ARG ALA ILE LEU GLU TYR LEU SEQRES 10 A 124 ARG GLN VAL ALA GLU ASN GLN HET SO4 A 201 5 HET HEC A 202 43 HETNAM SO4 SULFATE ION HETNAM HEC HEME C FORMUL 2 SO4 O4 S 2- FORMUL 3 HEC C34 H34 FE N4 O4 FORMUL 4 HOH *168(H2 O) HELIX 1 1 ASP A 9 GLY A 18 1 10 HELIX 2 2 ASP A 30 CYS A 45 1 16 HELIX 3 3 ASP A 62 ARG A 67 1 6 HELIX 4 4 GLY A 68 ASN A 78 1 11 HELIX 5 5 ASN A 78 HIS A 86 1 9 HELIX 6 6 HIS A 86 GLY A 97 1 12 HELIX 7 7 SER A 106 GLN A 124 1 19 LINK SG CYS A 45 CAB HEC A 202 1555 1555 1.87 LINK SG CYS A 48 CAC HEC A 202 1555 1555 1.85 LINK NE2 HIS A 49 FE HEC A 202 1555 1555 2.02 LINK SD MET A 100 FE HEC A 202 1555 1555 2.34 CISPEP 1 GLY A 18 PRO A 19 0 9.62 SITE 1 AC1 6 GLU A 122 HOH A 368 HOH A 377 HOH A 425 SITE 2 AC1 6 HOH A 427 HOH A 437 SITE 1 AC2 16 TYR A 44 CYS A 45 CYS A 48 HIS A 49 SITE 2 AC2 16 ILE A 56 PRO A 58 ARG A 66 ARG A 67 SITE 3 AC2 16 TYR A 71 MET A 76 ILE A 83 LEU A 92 SITE 4 AC2 16 THR A 98 MET A 99 MET A 100 HOH A 324 CRYST1 39.592 32.644 42.064 90.00 94.56 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 0.025258 0.000000 0.002014 0.00000 SCALE2 0.000000 0.030633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023849 0.00000