HEADER ELECTRON TRANSPORT 01-MAR-73 1C2C OBSLTE 02-FEB-84 1C2C 2C2C TITLE THE STRUCTURE OF OXIDIZED CYTOCHROME $C=2= OF TITLE 2 RHODOSPIRILLUM RUBRUM COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.R.SALEMME,S.T.FREER,N.H.XUONG,R.A.ALDEN,J.KRAUT REVDAT 7 30-SEP-83 1C2C 1 REVDAT REVDAT 6 31-DEC-80 1C2C 1 REMARK REVDAT 5 07-APR-80 1C2C 3 SCALE ATOM REVDAT 4 20-JUL-78 1C2C 2 CONECT REVDAT 3 01-NOV-77 1C2C 1 COMPND SOURCE AUTHOR REMARK REVDAT 3 2 1 FORMUL REVDAT 2 03-JAN-77 1C2C 3 ATOM REVDAT 1 14-DEC-76 1C2C 0 JRNL AUTH F.R.SALEMME,S.T.FREER,N.H.XUONG,R.A.ALDEN,J.KRAUT JRNL TITL THE STRUCTURE OF OXIDIZED CYTOCHROME C=2= OF JRNL TITL 2 RHODOSPIRILLUM RUBRUM JRNL REF J.BIOL.CHEM. V. 248 3910 1973 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.R.SALEMME,S.T.FREER,R.A.ALDEN,J.KRAUT REMARK 1 TITL ATOMIC COORDINATES FOR FERRICYTOCHROME C=2= OF REMARK 1 TITL 2 RHODOSPIRILLUM RUBRUM REMARK 1 REF BIOCHEM.BIOPHYS.RES.COMM. V. 54 47 1973 REMARK 1 REFN ASTM BBRCA9 US ISSN 0006-291X REMARK 1 REFERENCE 2 REMARK 1 AUTH F.R.SALEMME,J.KRAUT,M.D.KAMEN REMARK 1 TITL STRUCTURAL BASES FOR FUNCTION IN CYTOCHROMES C, AN REMARK 1 TITL 2 INTERPRETATION OF COMPARATIVE X-RAY AND REMARK 1 TITL 3 BIOCHEMICAL DATA REMARK 1 REF J.BIOL.CHEM. V. 248 7701 1973 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 EDIT R.J.FELDMANN REMARK 1 REF ATLAS OF MACROMOLECULAR 110 1976 REMARK 1 REF 2 STRUCTURE ON MICROFICHE REMARK 1 PUBL TRACOR JITCO INC.,ROCKVILLE,MD. REMARK 1 REFN ISBN 0-917934-01-6 REMARK 1 REFERENCE 4 REMARK 1 EDIT M.O.DAYHOFF REMARK 1 REF ATLAS OF PROTEIN SEQUENCE V. 5 44 1976 REMARK 1 REF 2 AND STRUCTURE,SUPPLEMENT 2 REMARK 1 PUBL NATIONAL BIOMEDICAL RESEARCH FOUNDATION, SILVER REMARK 1 PUBL 2 SPRING,MD. REMARK 1 REFN ISSN 0-912466-05-7 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 : 861 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 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 1C2C COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 1C2C CORRECTION. REFORMAT HEADER INFORMATION TO MEET NEW REMARK 5 1C2C SPECIFICATIONS. 1C2C ADD FORMUL RECORDS. 1C2C 01-NOV- REMARK 5 77. 1C2C REMARK 6 REMARK 6 1C2C CORRECTION. FIX TWO CONECT RECORDS. 20-JUL-78. 1C2C REMARK 7 REMARK 7 1C2C CORRECTION. STANDARDIZE NOMENCLATURE TO FOLLOW IUPAC- REMARK 7 IUB 1C2C RECOMMENDATIONS. INTERCHANGE CD1 AND CD2 FOR REMARK 7 LEUCINES 1C2C 32, 67, 79, 95, 108. INTERCHANGE CG1 AND CG2 REMARK 7 FOR VALINES 1C2C 10, 78. CORRECT SCALE MATRIX. 07-APR-80. REMARK 7 1C2C REMARK 8 REMARK 8 1C2C CORRECTION. STANDARDIZE FORMAT OF REMARK 2. 31-DEC-80. REMARK 8 1C2C REMARK 9 REMARK 9 1C2C CORRECTION. INSERT REVDAT RECORDS. 30-SEP-83. 1C2C REMARK 10 REMARK 10 1C2C CORRECTION. THIS ENTRY IS OBSOLETE. 14-FEB-84. 1C2C 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 (%): 40.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 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 16.11000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.31000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.31000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.11000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.68000 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 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 REMARK 500 SG CYS 14 CAB HEM 1 1.68 REMARK 500 NE2 HIS 18 FE HEM 1 1.78 REMARK 500 O LYS 97 CG1 ILE 101 1.80 REMARK 500 O TYR 107 N LYS 109 1.80 REMARK 500 O ASP 84 N LYS 86 1.89 REMARK 500 O LYS 56 N LYS 58 1.90 REMARK 500 SG CYS 17 CBC HEM 1 2.03 REMARK 500 O VAL 71 N ASN 73 2.05 REMARK 500 O MET 55 N GLY 59 2.13 REMARK 500 ND1 HIS 18 CD1 LEU 32 2.14 REMARK 500 O VAL 104 CB LEU 108 2.14 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS 12 CD LYS 109 4546 0.91 REMARK 500 CG LYS 12 NZ LYS 109 4546 1.15 REMARK 500 CD LYS 12 CE LYS 109 4546 1.32 REMARK 500 CD LYS 12 NZ LYS 109 4546 1.37 REMARK 500 CB ALA 57 O ALA 65 3755 1.50 REMARK 500 NZ LYS 12 CG LYS 109 4546 1.54 REMARK 500 CE LYS 12 CD LYS 109 4546 1.59 REMARK 500 CE LYS 12 CE LYS 109 4546 1.64 REMARK 500 CB ALA 57 C ALA 65 3755 1.67 REMARK 500 CE LYS 12 NZ LYS 109 4546 1.72 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 M RES CSSEQI PSI PHI REMARK 500 ALA 16 -47.33 137.83 REMARK 500 LYS 27 19.73 18.07 REMARK 500 PHE 36 -116.71 -4.20 REMARK 500 HIS 42 -125.79 -6.16 REMARK 500 LYS 58 -53.24 139.78 REMARK 500 GLU 64 -48.47 119.49 REMARK 500 LYS 72 -70.75 44.36 REMARK 500 PHE 77 -38.12 113.58 REMARK 500 THR 92 129.22 84.77 REMARK 500 LYS 94 -138.00 -28.43 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU 1 GLY 2 124.54 REMARK 500 LEU 67 ALA 68 148.28 REMARK 500 LYS 75 ALA 76 147.03 REMARK 500 GLY 83 ASP 84 149.60 REMARK 500 GLU 102 ASN 103 143.40 REMARK 500 ASN 103 VAL 104 -149.83 REMARK 500 ALA 106 TYR 107 146.37 SEQRES 1 112 GLU GLY ASP ALA ALA ALA GLY GLU LYS VAL SER LYS LYS SEQRES 2 112 CYS LEU ALA CYS HIS THR PHE ASP GLN GLY GLY ALA ASN SEQRES 3 112 LYS VAL GLY PRO ASN LEU PHE GLY VAL PHE GLU ASN THR SEQRES 4 112 ALA ALA HIS LYS ASP ASN TYR ALA TYR SER GLU SER TYR SEQRES 5 112 THR GLU MET LYS ALA LYS GLY LEU THR TRP THR GLU ALA SEQRES 6 112 ASN LEU ALA ALA TYR VAL LYS ASN PRO LYS ALA PHE VAL SEQRES 7 112 LEU GLU LYS SER GLY ASP PRO LYS ALA LYS SER LYS MET SEQRES 8 112 THR PHE LYS LEU THR LYS ASP ASP GLU ILE GLU ASN VAL SEQRES 9 112 ILE ALA TYR LEU LYS THR LEU LYS HET HEM 1 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 HELIX 1 H1 GLY 2 VAL 10 1CONTIGUOUS WITH HELIX H2 9 HELIX 2 H2 VAL 10 HIS 18 5CONTIGUOUS WITH HELIX H1 9 HELIX 3 H3 GLU 50 ALA 57 5 8 HELIX 4 H4 GLU 64 VAL 71 1 8 HELIX 5 H5 LYS 75 GLU 80 1 6 HELIX 6 H6 THR 96 THR 110 1 15 TURN 1 T1 VAL 10 LYS 13 TYPE I(10) TURN 2 T2 SER 11 CYS 14 TYPE I(10) CYS 14 BOUND TO HEM TURN 3 T3 ASP 21 GLY 24 TYPE II(10) TURN 4 T5 VAL 35 ASN 38 TYPE I(10) CRYST1 32.220 37.360 84.620 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 0.869026 0.000000 0.000000 0.00000 ORIGX2 0.000000 0.856531 0.000000 0.00000 ORIGX3 0.000000 0.000000 0.850863 0.00000 SCALE1 0.031037 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026767 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011818 0.00000