HEADER ELECTRON TRANSPORT 18-MAY-00 1F1F
TITLE CRYSTAL STRUCTURE OF CYTOCHROME C6 FROM ARTHROSPIRA MAXIMA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CYTOCHROME C6;
COMPND 3 CHAIN: A
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ARTHROSPIRA MAXIMA;
SOURCE 3 ORGANISM_TAXID: 129910
KEYWDS CYTOCHROME C6, HEME, PROTEIN STRUCTURE, CYANOBACTERIA,
KEYWDS 2 PHOTOSYNTHESIS, ELECTRON TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR C.A.KERFELD,A.A.SERAG,M.R.SAWAYA,D.W.KROGMANN,T.O.YEATES
REVDAT 5 03-MAR-21 1F1F 1 COMPND REMARK SEQADV HET
REVDAT 5 2 1 HETNAM HETSYN FORMUL LINK
REVDAT 5 3 1 ATOM
REVDAT 4 04-OCT-17 1F1F 1 REMARK
REVDAT 3 24-FEB-09 1F1F 1 VERSN
REVDAT 2 01-APR-03 1F1F 1 JRNL
REVDAT 1 08-AUG-01 1F1F 0
JRNL AUTH M.R.SAWAYA,D.W.KROGMANN,A.SERAG,K.K.HO,T.O.YEATES,
JRNL AUTH 2 C.A.KERFELD
JRNL TITL STRUCTURES OF CYTOCHROME C-549 AND CYTOCHROME C6 FROM THE
JRNL TITL 2 CYANOBACTERIUM ARTHROSPIRA MAXIMA.
JRNL REF BIOCHEMISTRY V. 40 9215 2001
JRNL REFN ISSN 0006-2960
JRNL PMID 11478889
JRNL DOI 10.1021/BI002679P
REMARK 2
REMARK 2 RESOLUTION. 2.70 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) : 2.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
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) (%) : 80.4
REMARK 3 NUMBER OF REFLECTIONS : 7504
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : 5% RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.232
REMARK 3 FREE R VALUE : 0.255
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 344
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 : 643
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 43
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 27.60
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) : 0.011
REMARK 3 BOND ANGLES (DEGREES) : 1.217
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 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 1F1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-00.
REMARK 100 THE DEPOSITION ID IS D_1000011125.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-JUN-95
REMARK 200 TEMPERATURE (KELVIN) : 298.0
REMARK 200 PH : 7.8
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) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7504
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 80.8
REMARK 200 DATA REDUNDANCY : 3.200
REMARK 200 R MERGE (I) : 0.08600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00
REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): NULL
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 7.8, 2.4 M (NH4)2SO4,
REMARK 280 0.5 M LISO4, 1% GLYCEROL, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 298.0K
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 39.70000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.85000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.90000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.85000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.70000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.90000
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 GLY A 1
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 ARG A 22 -158.74 -105.45
REMARK 500 LYS A 29 52.33 -114.68
REMARK 500 ASN A 60 -123.24 46.30
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 HEC A 200 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 18 NE2
REMARK 620 2 HEC A 200 NA 92.4
REMARK 620 3 HEC A 200 NB 91.1 91.7
REMARK 620 4 HEC A 200 NC 86.9 179.3 88.6
REMARK 620 5 HEC A 200 ND 85.9 90.2 176.4 89.4
REMARK 620 6 MET A 62 SD 170.5 95.4 94.1 85.3 88.7
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 HEC A 200
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1CYI RELATED DB: PDB
REMARK 900 1CYI CONTAINS CRYSTAL STRUCTURE OF CYTOCHROME C6 FROM CHLAMYDOMONAS
REMARK 900 REINHARDTII
DBREF 1F1F A 1 89 UNP P00118 CYC6_SPIMA 1 89
SEQADV 1F1F LEU A 72 UNP P00118 LYS 72 CONFLICT
SEQRES 1 A 89 GLY ASP VAL ALA ALA GLY ALA SER VAL PHE SER ALA ASN
SEQRES 2 A 89 CYS ALA ALA CYS HIS MET GLY GLY ARG ASN VAL ILE VAL
SEQRES 3 A 89 ALA ASN LYS THR LEU SER LYS SER ASP LEU ALA LYS TYR
SEQRES 4 A 89 LEU LYS GLY PHE ASP ASP ASP ALA VAL ALA ALA VAL ALA
SEQRES 5 A 89 TYR GLN VAL THR ASN GLY LYS ASN ALA MET PRO GLY PHE
SEQRES 6 A 89 ASN GLY ARG LEU SER PRO LEU GLN ILE GLU ASP VAL ALA
SEQRES 7 A 89 ALA TYR VAL VAL ASP GLN ALA GLU LYS GLY TRP
HET HEC A 200 43
HETNAM HEC HEME C
FORMUL 2 HEC C34 H34 FE N4 O4
HELIX 1 1 ASP A 2 CYS A 14 1 13
HELIX 2 2 CYS A 14 MET A 19 1 6
HELIX 3 3 GLY A 20 ARG A 22 5 3
HELIX 4 4 SER A 32 LEU A 40 1 9
HELIX 5 5 ASP A 46 GLY A 58 1 13
HELIX 6 6 SER A 70 GLY A 88 1 19
LINK SG CYS A 14 CAB HEC A 200 1555 1555 1.83
LINK SG CYS A 17 CAC HEC A 200 1555 1555 1.83
LINK NE2 HIS A 18 FE HEC A 200 1555 1555 2.02
LINK SD MET A 62 FE HEC A 200 1555 1555 2.33
SITE 1 AC1 18 ASN A 13 CYS A 14 CYS A 17 HIS A 18
SITE 2 AC1 18 ASN A 23 LYS A 29 THR A 30 LEU A 31
SITE 3 AC1 18 ASP A 35 LEU A 36 TYR A 39 GLN A 54
SITE 4 AC1 18 VAL A 55 LYS A 59 ASN A 60 ALA A 61
SITE 5 AC1 18 MET A 62 GLU A 86
CRYST1 79.400 67.800 49.700 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 0.012594 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014749 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020121 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
