HEADER HEME PROTEIN OF ELECTRON TRANSPORT 19-JAN-82 1CDV OBSLTE 02-FEB-84 1CDV 2CDV TITLE ON CYTOCHROME $C=3= FOLDING COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS HEME PROTEIN OF ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Y.HIGUCHI,N.YASUOKA,M.KAKUDO REVDAT 3 31-JAN-84 1CDV 1 REMARK REVDAT 2 30-SEP-83 1CDV 1 REVDAT REVDAT 1 15-APR-82 1CDV 0 JRNL AUTH Y.HIGUCHI,M.KUSUNOKI,N.YASUOKA,M.KAKUDO,T.YAGI JRNL TITL ON CYTOCHROME C=3= FOLDING JRNL REF J.BIOCHEM.(TOKYO) V. 90 1715 1981 JRNL REFN ASTM JOBIAO JA ISSN 0021-924X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.HIGUCHI,S.BANDO,M.KUSUNOKI,Y.MATSUURA,N.YASUOKA, REMARK 1 AUTH 2 M.KAKUDO,T.YAMANAKA,T.YAGI,H.INOKUCHI REMARK 1 TITL THE STRUCTURE OF CYTOCHROME C=3= FROM REMARK 1 TITL 2 DESULFOVIBRIO VULGARIS MIYAZAKI AT 2.5 ANGSTROMS REMARK 1 TITL 3 RESOLUTION REMARK 1 REF J.BIOCHEM.(TOKYO) V. 89 1659 1981 REMARK 1 REFN ASTM JOBIAO JA ISSN 0021-924X REMARK 1 REFERENCE 2 REMARK 1 AUTH W.SHINKAI,T.HASE,T.YAGI,H.MATSUBARA REMARK 1 TITL AMINO ACID SEQUENCE OF CYTOCHROME C=3= FROM REMARK 1 TITL 2 DESULFOVIBRIO VULGARIS, MIYAZAKI REMARK 1 REF J.BIOCHEM.(TOKYO) V. 87 1747 1980 REMARK 1 REFN ASTM JOBIAO JA ISSN 0021-924X REMARK 1 REFERENCE 3 REMARK 1 AUTH S.BANDO,Y.MATSUURA,N.TANAKA,N.YASUOKA,M.KAKUDO, REMARK 1 AUTH 2 T.YAGI,H.INOKUCHI REMARK 1 TITL CRYSTALLOGRAPHIC DATA FOR CYTOCHROME C=3= FROM TWO REMARK 1 TITL 2 STRAINS OF DESULFOVIBRIO VULGARIS, MIYAZAKI REMARK 1 REF J.BIOCHEM.(TOKYO) V. 86 269 1979 REMARK 1 REFN ASTM JOBIAO JA ISSN 0021-924X REMARK 2 REMARK 2 RESOLUTION. NULL ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL 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 : NULL 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) : NULL 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 : 107 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 172 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 1CDV COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 1CDV CORRECTION. CORRECT JOURNAL NAME FOR REFERENCES 1, 2, REMARK 5 3, 4. 1CDV 31-JAN-84. 1CDV REMARK 6 REMARK 6 1CDV THIS ENTRY IS OBSOLETE. 14-FEB-84. 1CDV REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-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 SMTRY1 2 -1.000000 0.000000 0.000000 26.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.45000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.45000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ALA 1 N C O CB REMARK 470 PRO 2 N C O CB CG CD REMARK 470 LYS 3 N C O CB CG CD CE REMARK 470 LYS 3 NZ REMARK 470 ALA 4 N C O CB REMARK 470 PRO 5 N C O CB CG CD REMARK 470 ALA 6 N C O CB REMARK 470 ASP 7 N C O CB CG OD1 OD2 REMARK 470 GLY 8 N C O REMARK 470 LEU 9 N C O CB CG CD1 CD2 REMARK 470 LYS 10 N C O CB CG CD CE REMARK 470 LYS 10 NZ REMARK 470 MET 11 N C O CB CG SD CE REMARK 470 ASP 12 N C O CB CG OD1 OD2 REMARK 470 LYS 13 N C O CB CG CD CE REMARK 470 LYS 13 NZ REMARK 470 THR 14 N C O CB OG1 CG2 REMARK 470 LYS 15 N C O CB CG CD CE REMARK 470 LYS 15 NZ REMARK 470 GLN 16 N C O CB CG CD OE1 REMARK 470 GLN 16 NE2 REMARK 470 PRO 17 N C O CB CG CD REMARK 470 VAL 18 N C O CB CG1 CG2 REMARK 470 VAL 19 N C O CB CG1 CG2 REMARK 470 PHE 20 N C O CB CG CD1 CD2 REMARK 470 PHE 20 CE1 CE2 CZ REMARK 470 ASN 21 N C O CB CG OD1 ND2 REMARK 470 HIS 22 N C O CB CG ND1 CD2 REMARK 470 HIS 22 CE1 NE2 REMARK 470 SER 23 N C O CB OG REMARK 470 THR 24 N C O CB OG1 CG2 REMARK 470 HIS 25 N C O CB CG ND1 CD2 REMARK 470 HIS 25 CE1 NE2 REMARK 470 LYS 26 N C O CB CG CD CE REMARK 470 LYS 26 NZ REMARK 470 ALA 27 N C O CB REMARK 470 VAL 28 N C O CB CG1 CG2 REMARK 470 LYS 29 N C O CB CG CD CE REMARK 470 LYS 29 NZ REMARK 470 CYS 30 N C O CB SG REMARK 470 GLY 31 N C O REMARK 470 ASP 32 N C O CB CG OD1 OD2 REMARK 470 CYS 33 N C O CB SG REMARK 470 HIS 34 N C O CB CG ND1 CD2 REMARK 470 HIS 34 CE1 NE2 REMARK 470 HIS 35 N C O CB CG ND1 CD2 REMARK 470 HIS 35 CE1 NE2 REMARK 470 PRO 36 N C O CB CG CD REMARK 470 VAL 37 N C O CB CG1 CG2 REMARK 470 ASN 38 N C O CB CG OD1 ND2 REMARK 470 GLY 39 N C O REMARK 470 LYS 40 N C O CB CG CD CE REMARK 470 LYS 40 NZ REMARK 470 GLU 41 N C O CB CG CD OE1 REMARK 470 GLU 41 OE2 REMARK 470 ASN 42 N C O CB CG OD1 ND2 REMARK 470 TYR 43 N C O CB CG CD1 CD2 REMARK 470 TYR 43 CE1 CE2 CZ OH REMARK 470 GLN 44 N C O CB CG CD OE1 REMARK 470 GLN 44 NE2 REMARK 470 LYS 45 N C O CB CG CD CE REMARK 470 LYS 45 NZ REMARK 470 CYS 46 N C O CB SG REMARK 470 ALA 47 N C O CB REMARK 470 THR 48 N C O CB OG1 CG2 REMARK 470 ALA 49 N C O CB REMARK 470 GLY 50 N C O REMARK 470 CYS 51 N C O CB SG REMARK 470 HIS 52 N C O CB CG ND1 CD2 REMARK 470 HIS 52 CE1 NE2 REMARK 470 ASP 53 N C O CB CG OD1 OD2 REMARK 470 ASN 54 N C O CB CG OD1 ND2 REMARK 470 MET 55 N C O CB CG SD CE REMARK 470 ASP 56 N C O CB CG OD1 OD2 REMARK 470 LYS 57 N C O CB CG CD CE REMARK 470 LYS 57 NZ REMARK 470 LYS 58 N C O CB CG CD CE REMARK 470 LYS 58 NZ REMARK 470 ASP 59 N C O CB CG OD1 OD2 REMARK 470 LYS 60 N C O CB CG CD CE REMARK 470 LYS 60 NZ REMARK 470 SER 61 N C O CB OG REMARK 470 ALA 62 N C O CB REMARK 470 LYS 63 N C O CB CG CD CE REMARK 470 LYS 63 NZ REMARK 470 GLY 64 N C O REMARK 470 TYR 65 N C O CB CG CD1 CD2 REMARK 470 TYR 65 CE1 CE2 CZ OH REMARK 470 TYR 66 N C O CB CG CD1 CD2 REMARK 470 TYR 66 CE1 CE2 CZ OH REMARK 470 HIS 67 N C O CB CG ND1 CD2 REMARK 470 HIS 67 CE1 NE2 REMARK 470 ALA 68 N C O CB REMARK 470 MET 69 N C O CB CG SD CE REMARK 470 HIS 70 N C O CB CG ND1 CD2 REMARK 470 HIS 70 CE1 NE2 REMARK 470 ASP 71 N C O CB CG OD1 OD2 REMARK 470 LYS 72 N C O CB CG CD CE REMARK 470 LYS 72 NZ REMARK 470 GLY 73 N C O REMARK 470 THR 74 N C O CB OG1 CG2 REMARK 470 LYS 75 N C O CB CG CD CE REMARK 470 LYS 75 NZ REMARK 470 PHE 76 N C O CB CG CD1 CD2 REMARK 470 PHE 76 CE1 CE2 CZ REMARK 470 LYS 77 N C O CB CG CD CE REMARK 470 LYS 77 NZ REMARK 470 SER 78 N C O CB OG REMARK 470 CYS 79 N C O CB SG REMARK 470 VAL 80 N C O CB CG1 CG2 REMARK 470 GLY 81 N C O REMARK 470 CYS 82 N C O CB SG REMARK 470 HIS 83 N C O CB CG ND1 CD2 REMARK 470 HIS 83 CE1 NE2 REMARK 470 LEU 84 N C O CB CG CD1 CD2 REMARK 470 GLU 85 N C O CB CG CD OE1 REMARK 470 GLU 85 OE2 REMARK 470 THR 86 N C O CB OG1 CG2 REMARK 470 ALA 87 N C O CB REMARK 470 GLY 88 N C O REMARK 470 ALA 89 N C O CB REMARK 470 ASP 90 N C O CB CG OD1 OD2 REMARK 470 ALA 91 N C O CB REMARK 470 ALA 92 N C O CB REMARK 470 LYS 93 N C O CB CG CD CE REMARK 470 LYS 93 NZ REMARK 470 LYS 94 N C O CB CG CD CE REMARK 470 LYS 94 NZ REMARK 470 LYS 95 N C O CB CG CD CE REMARK 470 LYS 95 NZ REMARK 470 GLU 96 N C O CB CG CD OE1 REMARK 470 GLU 96 OE2 REMARK 470 LEU 97 N C O CB CG CD1 CD2 REMARK 470 THR 98 N C O CB OG1 CG2 REMARK 470 GLY 99 N C O REMARK 470 CYS 100 N C O CB SG REMARK 470 LYS 101 N C O CB CG CD CE REMARK 470 LYS 101 NZ REMARK 470 GLY 102 N C O REMARK 470 SER 103 N C O CB OG REMARK 470 LYS 104 N C O CB CG CD CE REMARK 470 LYS 104 NZ REMARK 470 CYS 105 N C O CB SG REMARK 470 HIS 106 N C O CB CG ND1 CD2 REMARK 470 HIS 106 CE1 NE2 REMARK 470 SER 107 N C O CB OG SEQRES 1 107 ALA PRO LYS ALA PRO ALA ASP GLY LEU LYS MET ASP LYS SEQRES 2 107 THR LYS GLN PRO VAL VAL PHE ASN HIS SER THR HIS LYS SEQRES 3 107 ALA VAL LYS CYS GLY ASP CYS HIS HIS PRO VAL ASN GLY SEQRES 4 107 LYS GLU ASN TYR GLN LYS CYS ALA THR ALA GLY CYS HIS SEQRES 5 107 ASP ASN MET ASP LYS LYS ASP LYS SER ALA LYS GLY TYR SEQRES 6 107 TYR HIS ALA MET HIS ASP LYS GLY THR LYS PHE LYS SER SEQRES 7 107 CYS VAL GLY CYS HIS LEU GLU THR ALA GLY ALA ASP ALA SEQRES 8 107 ALA LYS LYS LYS GLU LEU THR GLY CYS LYS GLY SER LYS SEQRES 9 107 CYS HIS SER HET HEM 1 43 HET HEM 2 43 HET HEM 3 43 HET HEM 4 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM 4(C34 H32 FE N4 O4) HELIX 1 H1 SER 78 LEU 84 1 7 CRYST1 52.800 67.900 34.900 90.00 90.00 90.00 P 21 21 21 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 0.018939 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028653 0.00000