HEADER ELECTRON TRANSPORT (HEME PROTEIN) 01-JUL-80 4CYT OBSLTE 12-JUL-89 4CYT 5CYT TITLE REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME $C COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: R; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS ELECTRON TRANSPORT (HEME PROTEIN) EXPDTA X-RAY DIFFRACTION AUTHOR T.TAKANO REVDAT 5 12-JUL-89 4CYT 3 OBSLTE REVDAT 4 30-SEP-83 4CYT 1 REVDAT REVDAT 3 06-JAN-82 4CYT 1 JRNL REMARK REVDAT 2 04-DEC-80 4CYT 1 REMARK REVDAT 1 16-SEP-80 4CYT 0 SPRSDE 16-SEP-80 4CYT 2CYT JRNL AUTH T.TAKANO,R.E.DICKERSON JRNL TITL REDOX CONFORMATION CHANGES IN REFINED TUNA JRNL TITL 2 CYTOCHROME C JRNL REF PROC.NATL.ACAD.SCI.USA V. 77 6371 1980 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.TAKANO,R.E.DICKERSON REMARK 1 TITL CONFORMATION CHANGE OF CYTOCHROME C. I. REMARK 1 TITL 2 FERROCYTOCHROME C STRUCTURE REFINED AT 1.5 REMARK 1 TITL 3 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 153 79 1981 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.TAKANO,R.E.DICKERSON REMARK 1 TITL CONFORMATION CHANGE OF CYTOCHROME C. II. REMARK 1 TITL 2 FERRICYTOCHROME C REFINEMENT AT 1.8 ANGSTROMS AND REMARK 1 TITL 3 COMPARISON WITH THE FERROCYTOCHROME STRUCTURE REMARK 1 REF J.MOL.BIOL. V. 153 95 1981 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.E.DICKERSON REMARK 1 TITL CYTOCHROME C AND THE EVOLUTION OF ENERGY METABOLISM REMARK 1 REF SCI.AM. V. 242 136 1980 REMARK 1 REFN ASTM SCAMAC US ISSN 0036-8733 REMARK 1 REFERENCE 4 REMARK 1 AUTH S.H.NORTHRUP,M.R.PEAR,J.A.MCCAMMON,M.KARPLUS, REMARK 1 AUTH 2 T.TAKANO REMARK 1 TITL INTERNAL MOBILITY OF FERROCYTOCHROME C REMARK 1 REF NATURE V. 287 659 1980 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 5 REMARK 1 AUTH T.TAKANO,B.L.TRUS,N.MANDEL,G.MANDEL,O.B.KALLAI, REMARK 1 AUTH 2 R.SWANSON,R.E.DICKERSON REMARK 1 TITL TUNA CYTOCHROME C AT 2.0 ANGSTROMS RESOLUTION. II. REMARK 1 TITL 2 FERROCYTOCHROME STRUCTURE ANALYSIS REMARK 1 REF J.BIOL.CHEM. V. 252 776 1977 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 6 REMARK 1 AUTH R.SWANSON,B.L.TRUS,N.MANDEL,G.MANDEL,O.B.KALLAI, REMARK 1 AUTH 2 R.E.DICKERSON REMARK 1 TITL TUNA CYTOCHROME C AT 2.0 ANGSTROMS RESOLUTION. I. REMARK 1 TITL 2 FERRICYTOCHROME STRUCTURE ANALYSIS REMARK 1 REF J.BIOL.CHEM. V. 252 759 1977 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 7 REMARK 1 AUTH T.TAKANO,O.B.KALLAI,R.SWANSON,R.E.DICKERSON REMARK 1 TITL THE STRUCTURE OF FERROCYTOCHROME C AT 2.45 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 248 5234 1973 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 8 REMARK 1 AUTH R.E.DICKERSON REMARK 1 TITL THE STRUCTURE AND HISTORY OF AN ANCIENT PROTEIN REMARK 1 REF SCI.AM. V. 226 58 1972 REMARK 1 REFN ASTM SCAMAC US ISSN 0036-8733 REMARK 1 REFERENCE 9 REMARK 1 EDIT M.O.DAYHOFF REMARK 1 REF ATLAS OF PROTEIN SEQUENCE V. 5 39 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 : 803 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 54 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 4CYT COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 4CYT STRUCTURE FACTOR DATA FROM THIS ANALYSIS ARE AVAILABLE REMARK 5 FROM 4CYT THE PROTEIN DATA BANK AS A SEPARATE ENTRY REMARK 5 (R4CYTSF). 4CYT REMARK 6 REMARK 6 4CYT THE TRANSFORMATION WHICH WILL PLACE THE COORDINATES OF REMARK 6 4CYT THIS (REDUCED) MOLECULE INTO BEST ALIGNMENT WITH THOSE REMARK 6 OF 4CYT THE OXIDIZED INNER MOLECULE IN THE SPACE OF THE REMARK 6 LATTER IS 4CYT GIVEN BELOW 4CYT .2868 .8127 -.5072 47.2662 REMARK 6 4CYT .5553 -.5724 -.6033 17.5577 4CYT -.7806 -.1086 -.6155 REMARK 6 16.3160 4CYT REMARK 7 REMARK 7 4CYT CORRECTION. INSERT NEW PUBLICATION AS REFERENCE 3 AND REMARK 7 4CYT RENUMBER SUCCESSIVE REFERENCES. 04-DEC-80. 4CYT REMARK 8 REMARK 8 4CYT CORRECTION. UPDATE JRNL REFERENCE AND REFERENCE 1 TO REMARK 8 4CYT REFLECT PUBLICATION. INSERT NEW PUBLICATION AS REMARK 8 REFERENCE 4CYT 2 AND RENUMBER THE OTHERS. 06-JAN-82. 4CYT REMARK 9 REMARK 9 4CYT CORRECTION. INSERT REVDAT RECORDS. 30-SEP-83. 4CYT REMARK 10 REMARK 10 4CYT CORRECTION. THIS ENTRY IS OBSOLETE. 12-JUL-89. 4CYT 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 (%): 49.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 1/2-X,1/2+Y,-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 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 18.66500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.66500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.55000 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 350 APPLY THE FOLLOWING TO CHAINS: R 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 REMARK 500 NE2 HIS R 18 FE HEM R 1 1.97 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 R 88 NZ LYS R 88 2555 1.18 SEQRES 1 R 104 ACE GLY ASP VAL ALA LYS GLY LYS LYS THR PHE VAL GLN SEQRES 2 R 104 LYS CYS ALA GLN CYS HIS THR VAL GLU ASN GLY GLY LYS SEQRES 3 R 104 HIS LYS VAL GLY PRO ASN LEU TRP GLY LEU PHE GLY ARG SEQRES 4 R 104 LYS THR GLY GLN ALA GLU GLY TYR SER TYR THR ASP ALA SEQRES 5 R 104 ASN LYS SER LYS GLY ILE VAL TRP ASN ASN ASP THR LEU SEQRES 6 R 104 MET GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY SEQRES 7 R 104 THR LYS MET ILE PHE ALA GLY ILE LYS LYS LYS GLY GLU SEQRES 8 R 104 ARG GLN ASP LEU VAL ALA TYR LEU LYS SER ALA THR SER HET ACE R 0 3 HET HEM R 1 43 HETNAM ACE ACETYL GROUP HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 1 ACE C2 H4 O FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *54(H2 O1) HELIX 1 NR ASP R 2 CYS R 14 1 13 HELIX 2 50R THR R 49 LYS R 55 1 7 HELIX 3 60R ASN R 60 GLU R 69 1 10 HELIX 4 70R GLU R 69 ILE R 75 1INCOMPLETE DUE TO PRO 76 7 HELIX 5 CR LYS R 87 THR R 102 1 16 TURN 1 T1R GLU R 21 GLY R 24 TYPE II 3(10) TURN 2 T2R LEU R 32 LEU R 35 TYPE II 3(10) TURN 3 T3R LEU R 35 ARG R 38 TYPE II 3(10) TURN 4 T4R ALA R 43 TYR R 46 TYPE II 3(10) TURN 5 T5R ILE R 75 THR R 78 TYPE II 3(10) CRYST1 37.330 87.100 34.440 90.00 90.00 90.00 P 21 21 2 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 0.026788 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011481 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029036 0.00000 HETATM 1 C ACE R 0 -4.908 -1.959 10.948 1.00 26.26 C HETATM 2 O ACE R 0 -5.892 -2.598 10.550 1.00 23.47 O HETATM 3 CH3 ACE R 0 -4.713 -0.521 10.460 1.00 18.24 C