HEADER ELECTRON TRANSPORT 11-APR-02 1LFM TITLE CRYSTAL STRUCTURE OF COBALT(III)-SUBSTITUTED CYTOCHROME C (TUNA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THUNNUS THYNNUS; SOURCE 3 ORGANISM_COMMON: BLUEFIN TUNA; SOURCE 4 ORGANISM_TAXID: 8237; SOURCE 5 ORGANELLE: MITOCHONDRIA KEYWDS CYTOCHROME C, FOLDING, INTERMEDIATES, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.A.TEZCAN,W.M.FINDLEY,B.R.CRANE,S.A.ROSS,J.G.LYUBOVITSKY,H.B.GRAY, AUTHOR 2 J.R.WINKLER REVDAT 3 16-AUG-23 1LFM 1 REMARK LINK REVDAT 2 24-FEB-09 1LFM 1 VERSN REVDAT 1 19-JUL-02 1LFM 0 JRNL AUTH F.A.TEZCAN,W.M.FINDLEY,B.R.CRANE,S.A.ROSS,J.G.LYUBOVITSKY, JRNL AUTH 2 H.B.GRAY,J.R.WINKLER JRNL TITL USING DEEPLY TRAPPED INTERMEDIATES TO MAP THE CYTOCHROME C JRNL TITL 2 FOLDING LANDSCAPE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 8626 2002 JRNL REFN ISSN 0027-8424 JRNL PMID 12084923 JRNL DOI 10.1073/PNAS.132254499 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 27926 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2224 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3610 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 225 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1600 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 374 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 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) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.09 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.360 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1LFM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000015902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XFIT, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27926 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 15.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REFINEMENT REMARK 200 SOFTWARE USED: XFIT REMARK 200 STARTING MODEL: 3CYT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, NACL, NA3PO4, PH 6.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP AT 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 17.78050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.67075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 8.89025 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 DISTANCE REMARK 500 NE2 GLN A 42 O HOH A 476 1.96 REMARK 500 SG CYS A 14 CAB COH A 104 2.16 REMARK 500 SG CYS B 17 CAC COH B 104 2.17 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 27 -132.05 -110.03 REMARK 500 ASN A 70 87.87 -163.31 REMARK 500 LYS B 27 -134.53 -128.53 REMARK 500 ASN B 70 88.96 -164.10 REMARK 500 REMARK 500 REMARK: NULL 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 COH A 104 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 COH A 104 NA 89.7 REMARK 620 3 COH A 104 NB 89.2 91.2 REMARK 620 4 COH A 104 NC 90.5 178.5 90.2 REMARK 620 5 COH A 104 ND 88.3 86.9 176.9 91.6 REMARK 620 6 MET A 80 SD 170.4 83.0 97.2 96.6 85.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 COH B 104 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 18 NE2 REMARK 620 2 COH B 104 NA 93.0 REMARK 620 3 COH B 104 NB 85.5 89.5 REMARK 620 4 COH B 104 NC 92.2 173.2 86.7 REMARK 620 5 COH B 104 ND 94.6 91.7 178.8 92.2 REMARK 620 6 MET B 80 SD 175.5 82.7 93.1 92.0 87.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COH A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COH B 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I54 RELATED DB: PDB REMARK 900 RELATED ID: 1I55 RELATED DB: PDB REMARK 900 RELATED ID: 3CYT RELATED DB: PDB REMARK 900 RELATED ID: 5CYT RELATED DB: PDB DBREF 1LFM A 1 103 UNP P81459 CYC_THUAA 1 103 DBREF 1LFM B 1 103 UNP P81459 CYC_THUAA 1 103 SEQRES 1 A 103 GLY ASP VAL ALA LYS GLY LYS LYS THR PHE VAL GLN LYS SEQRES 2 A 103 CYS ALA GLN CYS HIS THR VAL GLU ASN GLY GLY LYS HIS SEQRES 3 A 103 LYS VAL GLY PRO ASN LEU TRP GLY LEU PHE GLY ARG LYS SEQRES 4 A 103 THR GLY GLN ALA GLU GLY TYR SER TYR THR ASP ALA ASN SEQRES 5 A 103 LYS SER LYS GLY ILE VAL TRP ASN ASN ASP THR LEU MET SEQRES 6 A 103 GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY THR SEQRES 7 A 103 LYS MET ILE PHE ALA GLY ILE LYS LYS LYS GLY GLU ARG SEQRES 8 A 103 GLN ASP LEU VAL ALA TYR LEU LYS SER ALA THR SER SEQRES 1 B 103 GLY ASP VAL ALA LYS GLY LYS LYS THR PHE VAL GLN LYS SEQRES 2 B 103 CYS ALA GLN CYS HIS THR VAL GLU ASN GLY GLY LYS HIS SEQRES 3 B 103 LYS VAL GLY PRO ASN LEU TRP GLY LEU PHE GLY ARG LYS SEQRES 4 B 103 THR GLY GLN ALA GLU GLY TYR SER TYR THR ASP ALA ASN SEQRES 5 B 103 LYS SER LYS GLY ILE VAL TRP ASN ASN ASP THR LEU MET SEQRES 6 B 103 GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY THR SEQRES 7 B 103 LYS MET ILE PHE ALA GLY ILE LYS LYS LYS GLY GLU ARG SEQRES 8 B 103 GLN ASP LEU VAL ALA TYR LEU LYS SER ALA THR SER HET COH A 104 43 HET COH B 104 43 HETNAM COH PROTOPORPHYRIN IX CONTAINING CO FORMUL 3 COH 2(C34 H32 CO N4 O4) FORMUL 5 HOH *374(H2 O) HELIX 1 1 ASP A 2 CYS A 14 1 13 HELIX 2 2 THR A 49 LYS A 55 1 7 HELIX 3 3 ASN A 60 ASN A 70 1 11 HELIX 4 4 ASN A 70 ILE A 75 1 6 HELIX 5 5 LYS A 87 THR A 102 1 16 HELIX 6 6 ASP B 2 CYS B 14 1 13 HELIX 7 7 THR B 49 LYS B 55 1 7 HELIX 8 8 ASN B 60 ASN B 70 1 11 HELIX 9 9 ASN B 70 ILE B 75 1 6 HELIX 10 10 LYS B 87 THR B 102 1 16 LINK NE2 HIS A 18 CO COH A 104 1555 1555 2.05 LINK SD MET A 80 CO COH A 104 1555 1555 2.38 LINK NE2 HIS B 18 CO COH B 104 1555 1555 2.01 LINK SD MET B 80 CO COH B 104 1555 1555 2.40 SITE 1 AC1 23 LYS A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC1 23 VAL A 28 GLY A 29 PRO A 30 THR A 40 SITE 3 AC1 23 GLY A 41 TYR A 46 TYR A 48 THR A 49 SITE 4 AC1 23 ASN A 52 LYS A 55 TRP A 59 TYR A 67 SITE 5 AC1 23 THR A 78 LYS A 79 MET A 80 ILE A 81 SITE 6 AC1 23 PHE A 82 HOH A 219 HOH A 281 SITE 1 AC2 21 LYS B 13 CYS B 14 CYS B 17 HIS B 18 SITE 2 AC2 21 VAL B 28 GLY B 29 PRO B 30 THR B 40 SITE 3 AC2 21 GLY B 41 TYR B 46 TYR B 48 THR B 49 SITE 4 AC2 21 ASN B 52 LYS B 55 TRP B 59 TYR B 67 SITE 5 AC2 21 THR B 78 LYS B 79 MET B 80 PHE B 82 SITE 6 AC2 21 HOH B 327 CRYST1 74.175 74.175 35.561 90.00 90.00 90.00 P 43 8 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 0.013482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028121 0.00000