HEADER ELECTRON TRANSPORT 05-APR-12 4EIC
TITLE CRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM SYNECHOCOCCUS SP. PCC
TITLE 2 7002 AT ULTRA-HIGH RESOLUTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CYTOCHROME C6;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 25-117;
COMPND 5 SYNONYM: CYTOCHROME C-553, CYTOCHROME C553, SOLUBLE CYTOCHROME F;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS SP.;
SOURCE 3 ORGANISM_TAXID: 32049;
SOURCE 4 STRAIN: ATCC 27264 / PCC 7002 / PR-6;
SOURCE 5 GENE: PETJ, PETJ1, SYNPCC7002_A0167;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 668369;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5A;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PUCJ1;
SOURCE 11 OTHER_DETAILS: CO-EXPRESSION WITH PEC86
KEYWDS ELECTRON TRANSPORT, CYTOCHROME C6
EXPDTA X-RAY DIFFRACTION
AUTHOR S.KRZYWDA,W.BIALEK,M.JASKOLSKI,A.SZCZEPANIAK
REVDAT 3 13-SEP-23 4EIC 1 REMARK
REVDAT 2 10-MAR-21 4EIC 1 COMPND REMARK HET HETNAM
REVDAT 2 2 1 HETSYN FORMUL LINK ATOM
REVDAT 1 10-APR-13 4EIC 0
JRNL AUTH W.BIALEK,S.KRZYWDA,P.ZATWARNICKI,M.JASKOLSKI,A.SZCZEPANIAK
JRNL TITL CYTOCHROME C6 AND C6C FROM SYNECHOCOCCUS SP. PCC 7002 -
JRNL TITL 2 STRUCTURE AND FUNCTION.
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH W.BIALEK,S.KRZYWDA,M.JASKOLSKI,A.SZCZEPANIAK
REMARK 1 TITL ATOMIC-RESOLUTION STRUCTURE OF REDUCED CYANOBACTERIAL
REMARK 1 TITL 2 CYTOCHROME C6 WITH AN UNUSUAL SEQUENCE INSERTION.
REMARK 1 REF FEBS J. V. 276 4426 2009
REMARK 1 REFN ISSN 1742-464X
REMARK 1 PMID 19678839
REMARK 1 DOI 10.1111/J.1742-4658.2009.07150.X
REMARK 1 REFERENCE 2
REMARK 1 AUTH W.BIALEK,M.NELSON,K.TAMIOLA,T.KALLAS,A.SZCZEPANIAK
REMARK 1 TITL DEEPLY BRANCHING C6-LIKE CYTOCHROMES OF CYANOBACTERIA.
REMARK 1 REF BIOCHEMISTRY V. 47 5515 2008
REMARK 1 REFN ISSN 0006-2960
REMARK 1 PMID 18439023
REMARK 1 DOI 10.1021/BI701973G
REMARK 2
REMARK 2 RESOLUTION. 0.84 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELXL-97
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.84
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.55
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8
REMARK 3 CROSS-VALIDATION METHOD : FREE R
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.106
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.106
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.127
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 1.500
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 974
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 64908
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.095
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.095
REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.118
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 1.500
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 823
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 54437
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 662
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 55
REMARK 3 SOLVENT ATOMS : 120
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 800.71
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 664.26
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 12
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7849
REMARK 3 NUMBER OF RESTRAINTS : 7790
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.026
REMARK 3 ANGLE DISTANCES (A) : 0.057
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.004
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.115
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.093
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.025
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.080
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT, HYDROGENS HAVE
REMARK 3 BEEN ADDED IN THE RIDING POSITIONS
REMARK 4
REMARK 4 4EIC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-12.
REMARK 100 THE DEPOSITION ID IS D_1000071654.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 14-DEC-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
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) : 0.8166
REMARK 200 MONOCHROMATOR : GE
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64908
REMARK 200 RESOLUTION RANGE HIGH (A) : 0.840
REMARK 200 RESOLUTION RANGE LOW (A) : 32.550
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8
REMARK 200 DATA REDUNDANCY : 6.000
REMARK 200 R MERGE (I) : 0.06300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.84
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.86
REMARK 200 COMPLETENESS FOR SHELL (%) : 80.6
REMARK 200 DATA REDUNDANCY IN SHELL : 4.30
REMARK 200 R MERGE FOR SHELL (I) : 0.50700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.230
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 3DR0
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 39.09
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULPHATE, 0.1M MES, PH
REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K
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 13.84500
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 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 101 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 18 NE2
REMARK 620 2 HEC A 101 NA 91.1
REMARK 620 3 HEC A 101 NB 90.0 90.2
REMARK 620 4 HEC A 101 NC 88.7 179.6 90.1
REMARK 620 5 HEC A 101 ND 90.6 89.9 179.3 89.7
REMARK 620 6 MET A 65 SD 175.4 84.6 91.6 95.6 87.8
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 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 102
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3DR0 RELATED DB: PDB
REMARK 900 THE SAME PROTEIN AT 1.23 A RESOLUTION
REMARK 900 RELATED ID: 4EID RELATED DB: PDB
REMARK 900 RELATED ID: 4EIE RELATED DB: PDB
REMARK 900 RELATED ID: 4EIF RELATED DB: PDB
DBREF 4EIC A 1 93 UNP O30881 CYC6_SYNP2 25 117
SEQRES 1 A 93 ALA ASP ALA ALA ALA GLY ALA GLN VAL PHE ALA ALA ASN
SEQRES 2 A 93 CYS ALA ALA CYS HIS ALA GLY GLY ASN ASN ALA VAL MET
SEQRES 3 A 93 PRO THR LYS THR LEU LYS ALA ASP ALA LEU LYS THR TYR
SEQRES 4 A 93 LEU ALA GLY TYR LYS ASP GLY SER LYS SER LEU GLU GLU
SEQRES 5 A 93 ALA VAL ALA TYR GLN VAL THR ASN GLY GLN GLY ALA MET
SEQRES 6 A 93 PRO ALA PHE GLY GLY ARG LEU SER ASP ALA ASP ILE ALA
SEQRES 7 A 93 ASN VAL ALA ALA TYR ILE ALA ASP GLN ALA GLU ASN ASN
SEQRES 8 A 93 LYS TRP
HET HEC A 101 43
HET MES A 102 12
HETNAM HEC HEME C
HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
FORMUL 2 HEC C34 H34 FE N4 O4
FORMUL 3 MES C6 H13 N O4 S
FORMUL 4 HOH *120(H2 O)
HELIX 1 1 ASP A 2 CYS A 14 1 13
HELIX 2 2 CYS A 14 ALA A 19 1 6
HELIX 3 3 GLY A 20 ASN A 22 5 3
HELIX 4 4 LYS A 32 LEU A 40 1 9
HELIX 5 5 SER A 49 GLY A 61 1 13
HELIX 6 6 SER A 73 ASN A 90 1 18
LINK SG CYS A 14 CAB HEC A 101 1555 1555 1.83
LINK SG CYS A 17 CAC HEC A 101 1555 1555 1.84
LINK NE2 HIS A 18 FE HEC A 101 1555 1555 1.98
LINK SD MET A 65 FE HEC A 101 1555 1555 2.34
SITE 1 AC1 20 ASN A 13 CYS A 14 CYS A 17 HIS A 18
SITE 2 AC1 20 ASN A 23 VAL A 25 MET A 26 LYS A 29
SITE 3 AC1 20 THR A 30 LEU A 31 ALA A 35 TYR A 39
SITE 4 AC1 20 LEU A 40 GLN A 57 VAL A 58 GLN A 62
SITE 5 AC1 20 MET A 65 HOH A 201 HOH A 215 HOH A 268
SITE 1 AC2 1 CYS A 17
CRYST1 31.860 27.690 44.070 90.00 101.10 90.00 P 1 21 1 2
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 0.031387 0.000000 0.006128 0.00000
SCALE2 0.000000 0.036114 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023120 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
