10 20 30 40 50 60 70 80 1JDL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 14-JUN-01 1JDL
TITLE STRUCTURE OF CYTOCHROME C2 FROM RHODOSPIRILLUM CENTENUM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C2, ISO-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: C552
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOSPIRILLUM CENTENUM; SOURCE 3 ORGANISM_TAXID: 34018
KEYWDS ALPHA HELIX, ELECTRON TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR A.CAMARA-ARTIGAS,J.C.WILLIAMS,J.P.ALLEN
REVDAT 2 24-FEB-09 1JDL 1 VERSN REVDAT 1 07-NOV-01 1JDL 0
JRNL AUTH A.CAMARA-ARTIGAS,J.C.WILLIAMS,J.P.ALLEN JRNL TITL STRUCTURE OF CYTOCHROME C2 FROM RHODOSPIRILLUM JRNL TITL 2 CENTENUM. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 1498 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11679712 JRNL DOI 10.1107/S0907444901010423
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.WANG,X.LI,J.C.WILLIAMS,J.P.ALLEN,P.MATHIS REMARK 1 TITL INTERACTION BETWEEN CYTOCHROME C2 AND REACTION REMARK 1 TITL 2 CENTERS FROM PURPLE BACTERIA REMARK 1 REF BIOCHEMISTRY V. 33 8306 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH X.LIN,J.C.WILLIAMS,J.P.ALLEN,P.MATHIS REMARK 1 TITL RELATIONSHIP BETWEEN RATE AND FREE ENERGY REMARK 1 TITL 2 DIFFERENCE FOR ELECTRON TRANSFER FROM CYTOCHROME REMARK 1 TITL 3 C2 TO THE REACTION CENTER IN RHODOBACTER REMARK 1 TITL 4 SPHAEROIDES. REMARK 1 REF BIOCHEMISTRY V. 33 13517 1994 REMARK 1 REFN ISSN 0006-2960
REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 12801 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) : 0.190 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1079 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2661 REMARK 3 BIN FREE R VALUE : 0.2626 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 81 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 : 892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.50000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -0.05000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.08 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.47 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 1JDL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-01. REMARK 100 THE RCSB ID CODE IS RCSB013655.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-99; 12-OCT-99; 15-OCT- REMARK 200 99 REMARK 200 TEMPERATURE (KELVIN) : 298; NULL; NULL REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; N; N REMARK 200 RADIATION SOURCE : ROTATING ANODE; ROTATING REMARK 200 ANODE; ROTATING ANODE REMARK 200 BEAMLINE : NULL; NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200HB; RIGAKU REMARK 200 RU200BH; RIGAKU RU200BH REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 1.5418; 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE; REMARK 200 IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC; RIGAKU REMARK 200 RAXIS IIC; RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13248 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 16.900 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2986.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 20.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 149.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD, MIR,MOLECULAR REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2C2C REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, POTASSIUM PHOSPHATE, PH REMARK 280 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
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 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 14.85000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.70000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.70000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.85000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.95000 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 1 REMARK 465 ASP A 2 REMARK 465 GLN A 121
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 LEU A 28 -132.70 -129.13 REMARK 500 ASP A 74 87.11 -166.69 REMARK 500 VAL A 99 72.43 -100.38 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 HEM A 500 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 19 NE2 REMARK 620 2 MET A 98 SD 172.4 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 500
DBREF 1JDL A 1 121 UNP P81154 CYC22_RHOCE 1 121
SEQRES 1 A 121 GLU ASP GLY ASP PRO ALA LYS GLY GLU ALA VAL PHE LYS SEQRES 2 A 121 LYS CYS MET ALA CYS HIS ARG VAL GLY PRO ASP ALA LYS SEQRES 3 A 121 ASN LEU VAL GLY PRO ALA LEU THR GLY VAL ILE ASP ARG SEQRES 4 A 121 GLN ALA GLY THR ALA PRO GLY PHE ASN TYR SER ALA ILE SEQRES 5 A 121 ASN HIS ALA ALA GLY GLU ALA GLY LEU HIS TRP THR PRO SEQRES 6 A 121 GLU ASN ILE ILE ALA TYR LEU PRO ASP PRO ASN ALA PHE SEQRES 7 A 121 LEU ARG LYS PHE LEU ALA ASP ALA GLY HIS ALA GLU GLN SEQRES 8 A 121 ALA LYS GLY SER THR LYS MET VAL PHE LYS LEU PRO ASP SEQRES 9 A 121 GLU GLN GLU ARG LYS ASP VAL VAL ALA TYR LEU LYS GLN SEQRES 10 A 121 PHE SER PRO GLN
HET HEM A 500 43
HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE
HETSYN HEM HEME
FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *87(H2 O)
HELIX 1 1 ASP A 4 PHE A 12 1 9 HELIX 2 2 LYS A 13 CYS A 15 5 3 HELIX 3 3 SER A 50 ALA A 59 1 10 HELIX 4 4 THR A 64 LEU A 72 1 9 HELIX 5 5 ASP A 74 ALA A 86 1 13 HELIX 6 6 HIS A 88 LYS A 93 5 6 HELIX 7 7 ASP A 104 LYS A 116 1 13 HELIX 8 8 GLN A 117 SER A 119 5 3
LINK NE2 HIS A 19 FE HEM A 500 1555 1555 2.10 LINK FE HEM A 500 SD MET A 98 1555 1555 2.32
SITE 1 AC1 22 LYS A 14 CYS A 15 CYS A 18 HIS A 19 SITE 2 AC1 22 VAL A 29 PRO A 31 ARG A 39 ALA A 41 SITE 3 AC1 22 GLY A 42 ASN A 48 TYR A 49 SER A 50 SITE 4 AC1 22 ASN A 53 TRP A 63 TYR A 71 THR A 96 SITE 5 AC1 22 LYS A 97 MET A 98 PHE A 100 LEU A 102 SITE 6 AC1 22 HOH A1009 HOH A1022
CRYST1 29.700 59.900 65.400 90.00 90.00 90.00 P 21 21 21 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 0.033670 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016694 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015291 0.00000