10 20 30 40 50 60 70 80 1F1C - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 18-MAY-00 1F1C
TITLE CRYSTAL STRUCTURE OF CYTOCHROME C549
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C549; COMPND 3 CHAIN: A, B
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTHROSPIRA MAXIMA; SOURCE 3 ORGANISM_TAXID: 129910
KEYWDS DIMERIC CYTOCHROME, ELECTRON TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR C.A.KERFELD,M.R.SAWAYA,T.O.YEATES,D.W.KROGMANN
REVDAT 3 24-FEB-09 1F1C 1 VERSN REVDAT 2 01-APR-03 1F1C 1 JRNL REVDAT 1 08-AUG-01 1F1C 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 JRNL TITL 2 FROM THE CYANOBACTERIUM ARTHROSPIRA MAXIMA. JRNL REF BIOCHEMISTRY V. 40 9215 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11478889 JRNL DOI 10.1021/BI002679P
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.W.KROGMANN REMARK 1 TITL THE LOW-POTENTIAL CYTOCHROME C OF CYANOBACTERIA REMARK 1 TITL 2 AND ALGAE REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V.1058 35 1991 REMARK 1 REFN ISSN 0006-3002 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.ALAM,J.SPRINKLE,M.A.HERMODSON,D.W.KROGMANN REMARK 1 TITL CHARACTERIZATION OF CYTOCHROME C-550 FROM REMARK 1 TITL 2 CYANOBACTERIA REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V. 766 317 1984 REMARK 1 REFN ISSN 0006-3002 REMARK 1 DOI 10.1016/0005-2728(84)90247-0
REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8556 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 866 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 : 2000 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.00 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.29 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 1F1C COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-00. REMARK 100 THE RCSB ID CODE IS RCSB011122.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-96 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 4.5 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8556 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.8 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.19000 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: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4M AMMONIUM ACETATE, PH 4.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 298.0K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 42.20000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 105 CZ NH1 NH2 REMARK 480 GLY A 131 OXT REMARK 480 ARG B 47 CZ NH1 NH2 REMARK 480 ASN B 53 CG OD1 ND2
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 ASN A 49 81.46 -158.42 REMARK 500 SER A 98 -7.99 -58.73 REMARK 500 ASN B 49 81.34 -158.58 REMARK 500 SER B 98 -7.58 -58.58 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 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 41 NE2 REMARK 620 2 HIS A 92 NE2 175.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 400 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 92 NE2 REMARK 620 2 HIS B 41 NE2 176.0 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 200 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 400
DBREF 1F1C A 3 131 UNP P82603 CY550_SPIMA 1 129 DBREF 1F1C B 3 131 UNP P82603 CY550_SPIMA 1 129
SEQRES 1 A 129 LEU THR GLU GLU LEU ARG THR PHE PRO ILE ASN ALA GLN SEQRES 2 A 129 GLY ASP THR ALA VAL LEU SER LEU LYS GLU ILE LYS LYS SEQRES 3 A 129 GLY GLN GLN VAL PHE ASN ALA ALA CYS ALA GLN CYS HIS SEQRES 4 A 129 ALA LEU GLY VAL THR ARG THR ASN PRO ASP VAL ASN LEU SEQRES 5 A 129 SER PRO GLU ALA LEU ALA LEU ALA THR PRO PRO ARG ASP SEQRES 6 A 129 ASN ILE ALA ALA LEU VAL ASP TYR ILE LYS ASN PRO THR SEQRES 7 A 129 THR TYR ASP GLY PHE VAL GLU ILE SER GLU LEU HIS PRO SEQRES 8 A 129 SER LEU LYS SER SER ASP ILE PHE PRO LYS MET ARG ASN SEQRES 9 A 129 ILE SER GLU ASP ASP LEU TYR ASN VAL ALA GLY TYR ILE SEQRES 10 A 129 LEU LEU GLN PRO LYS VAL ARG GLY GLU GLN TRP GLY SEQRES 1 B 129 LEU THR GLU GLU LEU ARG THR PHE PRO ILE ASN ALA GLN SEQRES 2 B 129 GLY ASP THR ALA VAL LEU SER LEU LYS GLU ILE LYS LYS SEQRES 3 B 129 GLY GLN GLN VAL PHE ASN ALA ALA CYS ALA GLN CYS HIS SEQRES 4 B 129 ALA LEU GLY VAL THR ARG THR ASN PRO ASP VAL ASN LEU SEQRES 5 B 129 SER PRO GLU ALA LEU ALA LEU ALA THR PRO PRO ARG ASP SEQRES 6 B 129 ASN ILE ALA ALA LEU VAL ASP TYR ILE LYS ASN PRO THR SEQRES 7 B 129 THR TYR ASP GLY PHE VAL GLU ILE SER GLU LEU HIS PRO SEQRES 8 B 129 SER LEU LYS SER SER ASP ILE PHE PRO LYS MET ARG ASN SEQRES 9 B 129 ILE SER GLU ASP ASP LEU TYR ASN VAL ALA GLY TYR ILE SEQRES 10 B 129 LEU LEU GLN PRO LYS VAL ARG GLY GLU GLN TRP GLY
HET HEM A 200 43 HET HEM B 400 43
HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE
HETSYN HEM HEME
FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *17(H2 O)
HELIX 1 1 SER A 22 CYS A 37 1 16 HELIX 2 2 CYS A 37 ALA A 42 1 6 HELIX 3 3 LEU A 43 VAL A 45 5 3 HELIX 4 4 SER A 55 LEU A 61 1 7 HELIX 5 5 ASN A 68 ASN A 78 1 11 HELIX 6 6 PHE A 101 ARG A 105 5 5 HELIX 7 7 SER A 108 GLY A 127 1 20 HELIX 8 8 GLU A 128 TRP A 130 5 3 HELIX 9 9 SER B 22 CYS B 37 1 16 HELIX 10 10 CYS B 37 ALA B 42 1 6 HELIX 11 11 LEU B 43 VAL B 45 5 3 HELIX 12 12 SER B 55 LEU B 61 1 7 HELIX 13 13 ASN B 68 ASN B 78 1 11 HELIX 14 14 PHE B 101 ARG B 105 5 5 HELIX 15 15 SER B 108 GLY B 127 1 20 HELIX 16 16 GLU B 128 TRP B 130 5 3
SHEET 1 A 2 THR A 9 PRO A 11 0 SHEET 2 A 2 THR A 18 VAL A 20 -1 O ALA A 19 N PHE A 10 SHEET 1 B 2 THR B 9 PRO B 11 0 SHEET 2 B 2 THR B 18 VAL B 20 -1 O ALA B 19 N PHE B 10
LINK FE HEM A 200 NE2 HIS A 41 1555 1555 2.16 LINK FE HEM A 200 NE2 HIS A 92 1555 1555 2.19 LINK SG CYS A 37 CAB HEM A 200 1555 1555 2.00 LINK SG CYS A 40 CAC HEM A 200 1555 1555 1.94 LINK FE HEM B 400 NE2 HIS B 92 1555 1555 2.29 LINK FE HEM B 400 NE2 HIS B 41 1555 1555 2.25
CISPEP 1 THR A 63 PRO A 64 0 0.01 CISPEP 2 THR B 63 PRO B 64 0 -0.28
SITE 1 AC1 18 ALA A 36 CYS A 37 GLN A 39 CYS A 40 SITE 2 AC1 18 HIS A 41 THR A 46 THR A 48 VAL A 52 SITE 3 AC1 18 ASN A 53 ALA A 62 TYR A 75 THR A 81 SITE 4 AC1 18 TYR A 82 HIS A 92 PRO A 93 HOH A 609 SITE 5 AC1 18 HOH A 614 GLU B 90 SITE 1 AC2 16 GLU A 90 ALA B 36 CYS B 37 GLN B 39 SITE 2 AC2 16 CYS B 40 HIS B 41 THR B 46 THR B 48 SITE 3 AC2 16 VAL B 52 ASN B 53 ALA B 62 TYR B 75 SITE 4 AC2 16 THR B 81 TYR B 82 HIS B 92 HOH B 616
CRYST1 36.500 84.400 43.800 90.00 96.50 90.00 P 1 21 1 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 0.027397 0.000000 0.003122 0.00000
SCALE2 0.000000 0.011848 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022979 0.00000