HEADER ELECTRON TRANSPORT 16-MAR-93 1CTH OBSLTE 24-DEC-97 1CTH 2CTH TITLE STRUCTURE ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO TITLE 2 VULGARIS HILDENBOROUGH AT 1.9 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR P.M.MATIAS,C.FRAZAO,J.MORAIS,M.COLL,M.A.CARRONDO REVDAT 1 31-OCT-93 1CTH 0 JRNL AUTH P.M.MATIAS,C.FRAZAO,J.MORAIS,M.COLL,M.A.CARRONDO JRNL TITL STRUCTURE ANALYSIS OF CYTOCHROME C3 FROM JRNL TITL 2 DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.9 JRNL TITL 3 ANGSTROM RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 1CTH REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 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) : 0.196 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 : 1620 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 344 REMARK 3 SOLVENT ATOMS : 83 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 2.70 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 1CTH COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 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 (%): 56.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,1/3+Z REMARK 290 3555 -X+Y,-X,2/3+Z REMARK 290 4555 -X,-Y,1/2+Z REMARK 290 5555 Y,-X+Y,5/6+Z REMARK 290 6555 X-Y,X,1/6+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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.73333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.46667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.60000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 64.33333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 12.86667 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 2 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: A, 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 REMARK 500 NE2 HIS B 35 FE HEM B 2 2.00 REMARK 500 NE2 HIS B 25 FE HEM B 3 2.02 REMARK 500 NE2 HIS B 70 FE HEM B 4 2.03 REMARK 500 NE2 HIS A 34 FE HEM A 1 2.06 REMARK 500 NE2 HIS A 35 FE HEM A 2 2.06 REMARK 500 NE2 HIS A 70 FE HEM A 4 2.06 REMARK 500 NE2 HIS B 52 FE HEM B 2 2.06 REMARK 500 NE2 HIS A 22 FE HEM A 1 2.07 REMARK 500 NE2 HIS A 106 FE HEM A 4 2.09 REMARK 500 NE2 HIS B 106 FE HEM B 4 2.09 REMARK 500 NE2 HIS B 34 FE HEM B 1 2.11 REMARK 500 NE2 HIS B 22 FE HEM B 1 2.12 REMARK 500 NE2 HIS B 83 FE HEM B 3 2.12 REMARK 500 NE2 HIS A 52 FE HEM A 2 2.14 REMARK 500 NE2 HIS A 83 FE HEM A 3 2.15 REMARK 500 NE2 HIS A 25 FE HEM A 3 2.17 SEQRES 1 A 107 ALA PRO LYS ALA PRO ALA ASP GLY LEU LYS MET GLU ALA SEQRES 2 A 107 THR LYS GLN PRO VAL VAL PHE ASN HIS SER THR HIS LYS SEQRES 3 A 107 SER VAL LYS CYS GLY ASP CYS HIS HIS PRO VAL ASN GLY SEQRES 4 A 107 LYS GLU ASP TYR ARG LYS CYS GLY THR ALA GLY CYS HIS SEQRES 5 A 107 ASP SER MET ASP LYS LYS ASP LYS SER ALA LYS GLY TYR SEQRES 6 A 107 TYR HIS VAL MET HIS ASP LYS ASN THR LYS PHE LYS SER SEQRES 7 A 107 CYS VAL GLY CYS HIS VAL GLU VAL ALA GLY ALA ASP ALA SEQRES 8 A 107 ALA LYS LYS LYS ASP LEU THR GLY CYS LYS LYS SER LYS SEQRES 9 A 107 CYS HIS GLU SEQRES 1 B 107 ALA PRO LYS ALA PRO ALA ASP GLY LEU LYS MET GLU ALA SEQRES 2 B 107 THR LYS GLN PRO VAL VAL PHE ASN HIS SER THR HIS LYS SEQRES 3 B 107 SER VAL LYS CYS GLY ASP CYS HIS HIS PRO VAL ASN GLY SEQRES 4 B 107 LYS GLU ASP TYR ARG LYS CYS GLY THR ALA GLY CYS HIS SEQRES 5 B 107 ASP SER MET ASP LYS LYS ASP LYS SER ALA LYS GLY TYR SEQRES 6 B 107 TYR HIS VAL MET HIS ASP LYS ASN THR LYS PHE LYS SER SEQRES 7 B 107 CYS VAL GLY CYS HIS VAL GLU VAL ALA GLY ALA ASP ALA SEQRES 8 B 107 ALA LYS LYS LYS ASP LEU THR GLY CYS LYS LYS SER LYS SEQRES 9 B 107 CYS HIS GLU HET HEM A 1 43 HET HEM A 2 43 HET HEM A 3 43 HET HEM A 4 43 HET HEM B 1 43 HET HEM B 2 43 HET HEM B 3 43 HET HEM B 4 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 8(C34 H32 FE N4 O4) FORMUL 11 HOH *83(H2 O1) HELIX 1 H1A HIS A 22 LYS A 26 5 5 HELIX 2 H2A LYS A 29 HIS A 34 1 6 HELIX 3 H3A TYR A 65 ASP A 71 1 7 HELIX 4 H4A SER A 78 ALA A 87 1 10 HELIX 5 H5A ALA A 91 GLY A 99 1 9 HELIX 6 H1B ASN B 21 LYS B 26 5 6 HELIX 7 H2B LYS B 29 CYS B 33 5 5 HELIX 8 H3B TYR B 65 ASP B 71 1 7 HELIX 9 H4B SER B 78 ALA B 87 1 10 HELIX 10 H5B ASP B 90 GLY B 99 1 10 SHEET 1 S1A 2 LEU A 9 MET A 11 0 SHEET 2 S1A 2 VAL A 18 PHE A 20 -1 SHEET 1 S1B 2 LEU B 9 MET B 11 0 SHEET 2 S1B 2 VAL B 18 PHE B 20 -1 SHEET 1 S2A 2 HIS A 35 PRO A 36 0 SHEET 2 S2A 2 GLU A 41 ASP A 42 -1 SHEET 1 S2B 2 HIS B 35 PRO B 36 0 SHEET 2 S2B 2 GLU B 41 ASP B 42 -1 TURN 1 T1A HIS A 25 VAL A 28 TURN 2 T2A VAL A 37 LYS A 40 TURN 3 T3A LYS A 45 THR A 48 TURN 4 T4A THR A 48 CYS A 51 TURN 5 T5A ASP A 56 ASP A 59 TURN 6 T6A SER A 61 GLY A 64 TURN 7 T7A ALA A 87 ASP A 90 TURN 8 T1B HIS B 25 VAL B 28 TURN 9 T2B VAL B 37 LYS B 40 TURN 10 T3B LYS B 45 THR B 48 TURN 11 T4B THR B 48 CYS B 51 TURN 12 T5B ASP B 56 ASP B 59 TURN 13 T6B SER B 61 GLY B 64 TURN 14 T7B ALA B 87 ASP B 90 CRYST1 77.000 77.000 77.200 90.00 90.00 120.00 P 61 12 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 0.012987 0.007498 0.000000 0.00000 SCALE2 0.000000 0.014996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012953 0.00000