HEADER ELECTRON TRANSPORT 08-AUG-95 1CTJ TITLE CRYSTAL STRUCTURE OF CYTOCHROME C6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C6; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MONORAPHIDIUM BRAUNII; SOURCE 3 ORGANISM_TAXID: 34112 KEYWDS CYTOCHROME, ELECTRON TRANSPORT, HEME EXPDTA X-RAY DIFFRACTION AUTHOR G.M.SHELDRICK REVDAT 2 24-FEB-09 1CTJ 1 VERSN REVDAT 1 10-JUN-96 1CTJ 0 JRNL AUTH C.FRAZAO,C.M.SOARES,M.A.CARRONDO,E.POHL,Z.DAUTER, JRNL AUTH 2 K.S.WILSON,M.HERVAS,J.A.NAVARRO,M.A.DE LA ROSA, JRNL AUTH 3 G.M.SHELDRICK JRNL TITL AB INITIO DETERMINATION OF THE CRYSTAL STRUCTURE JRNL TITL 2 OF CYTOCHROME C6 AND COMPARISON WITH PLASTOCYANIN. JRNL REF STRUCTURE V. 3 1159 1995 JRNL REFN ISSN 0969-2126 JRNL PMID 8591027 JRNL DOI 10.1016/S0969-2126(01)00252-0 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY 10TH REFLECTION REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.140 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.138 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3265 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 32653 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.120 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.118 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2428 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 24566 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 724 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 822.83 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 642.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 12 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 8268 REMARK 3 NUMBER OF RESTRAINTS : 10326 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.014 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.016 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.148 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.130 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.010 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.043 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.108 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL. V. 91 (1973) REMARK 3 201-228. REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE REMARK 3 R (NO CUTOFF) BY 0.077. CHEMICALLY EQUIVALENT BONDS AND ANGLE REMARK 3 DISTANCES IN HEME RESTRAINED TO BE EQUAL WITHOUT TARGET REMARK 3 VALUES. NO GEOMETRIC OR ADP RESTRAINTS APPLIED TO IRON ATOM. REMARK 4 REMARK 4 1CTJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAY-93 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.80, 0.87 REMARK 200 MONOCHROMATOR : GE(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32653 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELXL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 Z,X,Y REMARK 290 3555 Y,Z,X 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 0.169350 0.142732 0.975166 0.00000 REMARK 290 SMTRY2 2 0.985556 -0.024526 -0.167564 0.00000 REMARK 290 SMTRY3 2 0.000000 0.989457 -0.144824 0.00000 REMARK 290 SMTRY1 3 0.169350 0.985556 0.000000 0.00000 REMARK 290 SMTRY2 3 0.142732 -0.024526 0.989457 0.00000 REMARK 290 SMTRY3 3 0.975166 -0.167564 -0.144824 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 301 LIES ON A SPECIAL POSITION. 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 ASP A 3 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 3 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 3 C - N - CA ANGL. DEV. = 25.3 DEGREES REMARK 500 ASP A 42 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 GLY A 43 O - C - N ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG A 67 CD - NE - CZ ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 69 CB - CG - OD1 ANGL. DEV. = 6.1 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 LYS A 58 119.33 -163.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 223 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 233 DISTANCE = 5.38 ANGSTROMS REMARK 525 HOH A 253 DISTANCE = 7.74 ANGSTROMS 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 HEM A 91 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 19 NE2 REMARK 620 2 MET A 61 SD 175.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 91 DBREF 1CTJ A 1 89 UNP Q09099 CYC6_MONBR 1 89 SEQRES 1 A 89 GLU ALA ASP LEU ALA LEU GLY LYS ALA VAL PHE ASP GLY SEQRES 2 A 89 ASN CYS ALA ALA CYS HIS ALA GLY GLY GLY ASN ASN VAL SEQRES 3 A 89 ILE PRO ASP HIS THR LEU GLN LYS ALA ALA ILE GLU GLN SEQRES 4 A 89 PHE LEU ASP GLY GLY PHE ASN ILE GLU ALA ILE VAL TYR SEQRES 5 A 89 GLN ILE GLU ASN GLY LYS GLY ALA MET PRO ALA TRP ASP SEQRES 6 A 89 GLY ARG LEU ASP GLU ASP GLU ILE ALA GLY VAL ALA ALA SEQRES 7 A 89 TYR VAL TYR ASP GLN ALA ALA GLY ASN LYS TRP HET HEM A 91 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *151(H2 O) HELIX 1 1 LEU A 4 ASN A 14 1 11 HELIX 2 2 ALA A 16 GLY A 22 1 7 HELIX 3 3 LYS A 34 PHE A 40 1 7 HELIX 4 4 ILE A 47 ASN A 56 1 10 HELIX 5 5 GLU A 70 ALA A 85 1 16 LINK FE HEM A 91 NE2 HIS A 19 1555 1555 2.03 LINK FE HEM A 91 SD MET A 61 1555 1555 2.36 LINK CAB HEM A 91 SG CYS A 15 1555 1555 1.81 LINK CAC HEM A 91 SG CYS A 18 1555 1555 1.83 SITE 1 AC1 17 ASN A 14 CYS A 15 ALA A 17 CYS A 18 SITE 2 AC1 17 HIS A 19 ASN A 24 HIS A 30 THR A 31 SITE 3 AC1 17 LEU A 32 ALA A 36 PHE A 40 LEU A 41 SITE 4 AC1 17 GLN A 53 LYS A 58 MET A 61 HOH A 107 SITE 5 AC1 17 HOH A 239 CRYST1 40.430 40.430 40.430 80.25 80.25 80.25 R 3 3 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 0.024734 -0.004250 -0.003673 0.00000 SCALE2 0.000000 0.025097 -0.003673 0.00000 SCALE3 0.000000 0.000000 0.025364 0.00000