HEADER ELECTRON TRANSFER(IRON-SULFUR) 08-APR-91 1FXD
TITLE REFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIGAS AT
TITLE 2 1.7 ANGSTROMS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: FERREDOXIN II;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO GIGAS;
SOURCE 3 ORGANISM_TAXID: 879
KEYWDS ELECTRON TRANSFER(IRON-SULFUR)
EXPDTA X-RAY DIFFRACTION
AUTHOR C.R.KISSINGER,L.C.SIEKER,E.T.ADMAN,L.H.JENSEN
REVDAT 4 29-NOV-17 1FXD 1 HELIX
REVDAT 3 24-FEB-09 1FXD 1 VERSN
REVDAT 2 01-APR-03 1FXD 1 JRNL
REVDAT 1 15-APR-93 1FXD 0
JRNL AUTH C.R.KISSINGER,L.C.SIEKER,E.T.ADMAN,L.H.JENSEN
JRNL TITL REFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM
JRNL TITL 2 DESULFOVIBRIO GIGAS AT 1.7 A.
JRNL REF J.MOL.BIOL. V. 219 693 1991
JRNL REFN ISSN 0022-2836
JRNL PMID 2056535
JRNL DOI 10.1016/0022-2836(91)90665-S
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH C.R.KISSINGER,E.T.ADMAN,L.C.SIEKER,L.H.JENSEN,J.LEGALL
REMARK 1 TITL THE CRYSTAL STRUCTURE OF THE THREE-IRON FERREDOXIN II FROM
REMARK 1 TITL 2 DESULFOVIBRIO GIGAS
REMARK 1 REF FEBS LETT. V. 244 447 1989
REMARK 1 REFN ISSN 0014-5793
REMARK 1 REFERENCE 2
REMARK 1 AUTH C.R.KISSINGER,E.T.ADMAN,L.C.SIEKER,L.H.JENSEN
REMARK 1 TITL STRUCTURE OF THE 3FE-4S CLUSTER IN DESULFOVIBRIO GIGAS
REMARK 1 TITL 2 FERREDOXIN II
REMARK 1 REF J.AM.CHEM.SOC. V. 110 8721 1988
REMARK 1 REFN ISSN 0002-7863
REMARK 1 REFERENCE 3
REMARK 1 AUTH L.C.SIEKER,E.T.ADMAN,L.H.JENSEN,J.LEGALL
REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDY OF
REMARK 1 TITL 2 THE 3-FE FERREDOXIN II FROM THE BACTERIUM DESULFOVIBRIO
REMARK 1 TITL 3 GIGAS
REMARK 1 REF J.MOL.BIOL. V. 179 151 1984
REMARK 1 REFN ISSN 0022-2836
REMARK 2
REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PROFFT
REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : NULL
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : 0.157
REMARK 3 R VALUE (WORKING SET) : NULL
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 432
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 7
REMARK 3 SOLVENT ATOMS : 56
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
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 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : 0.020 ; NULL
REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : NULL ; NULL
REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL
REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : NULL ; NULL
REMARK 3 STAGGERED (DEGREES) : NULL ; NULL
REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1FXD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000173457.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
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: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 34.44
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 20.43500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.64000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 20.43500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.64000
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: DIMERIC
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 BIOMT1 2 -1.000000 0.000000 0.000000 34.15303
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 25.60358
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 113 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 119 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 122 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 125 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 136 LIES ON A SPECIAL POSITION.
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 CG GLU A 26 OE2 GLU A 44 3555 2.11
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 GLU A 3 OE1 - CD - OE2 ANGL. DEV. = 7.4 DEGREES
REMARK 500 GLU A 23 CA - CB - CG ANGL. DEV. = 17.3 DEGREES
REMARK 500 ASP A 29 CB - CG - OD1 ANGL. DEV. = 8.3 DEGREES
REMARK 500 GLU A 45 OE1 - CD - OE2 ANGL. DEV. = 8.0 DEGREES
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 F3S A 59 FE3
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 14 SG
REMARK 620 2 F3S A 59 S1 110.5
REMARK 620 3 F3S A 59 S3 116.4 104.2
REMARK 620 4 F3S A 59 S4 116.0 107.2 101.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 F3S A 59 FE4
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 50 SG
REMARK 620 2 F3S A 59 S2 110.4
REMARK 620 3 F3S A 59 S3 110.5 104.8
REMARK 620 4 F3S A 59 S4 121.4 105.0 103.4
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 F3S A 59 FE1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 8 SG
REMARK 620 2 F3S A 59 S1 106.0
REMARK 620 3 F3S A 59 S2 114.0 109.2
REMARK 620 4 F3S A 59 S3 118.8 105.1 103.3
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: FES
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: NULL
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F3S A 59
DBREF 1FXD A 1 58 UNP P00209 FER_DESGI 1 58
SEQADV 1FXD SCH A 11 UNP P00209 CYS 11 CONFLICT
SEQRES 1 A 58 PRO ILE GLU VAL ASN ASP ASP CYS MET ALA SCH GLU ALA
SEQRES 2 A 58 CYS VAL GLU ILE CYS PRO ASP VAL PHE GLU MET ASN GLU
SEQRES 3 A 58 GLU GLY ASP LYS ALA VAL VAL ILE ASN PRO ASP SER ASP
SEQRES 4 A 58 LEU ASP CYS VAL GLU GLU ALA ILE ASP SER CYS PRO ALA
SEQRES 5 A 58 GLU ALA ILE VAL ARG SER
MODRES 1FXD SCH A 11 CYS S-METHYL-THIO-CYSTEINE
HET SCH A 11 8
HET F3S A 59 7
HETNAM SCH S-METHYL-THIO-CYSTEINE
HETNAM F3S FE3-S4 CLUSTER
FORMUL 1 SCH C4 H9 N O2 S2
FORMUL 2 F3S FE3 S4
FORMUL 3 HOH *56(H2 O)
HELIX 1 A ALA A 13 ILE A 17 1 5
HELIX 2 B ASP A 41 SER A 49 1 9
SHEET 1 A 2 PRO A 1 VAL A 4 0
SHEET 2 A 2 ILE A 55 SER A 58 -1 O VAL A 56 N GLU A 3
SHEET 1 B 2 PHE A 22 MET A 24 0
SHEET 2 B 2 ALA A 31 VAL A 33 -1 N VAL A 32 O GLU A 23
SSBOND 1 CYS A 18 CYS A 42 1555 1555 1.98
LINK C ALA A 10 N SCH A 11 1555 1555 1.31
LINK C SCH A 11 N GLU A 12 1555 1555 1.32
LINK FE3 F3S A 59 SG CYS A 14 1555 1555 2.28
LINK FE4 F3S A 59 SG CYS A 50 1555 1555 2.22
LINK FE1 F3S A 59 SG CYS A 8 1555 1555 2.29
SITE 1 FES 3 CYS A 8 CYS A 14 CYS A 50
SITE 1 AC1 9 CYS A 8 MET A 9 ALA A 10 SCH A 11
SITE 2 AC1 9 GLU A 12 ALA A 13 CYS A 14 CYS A 50
SITE 3 AC1 9 ILE A 55
CRYST1 40.870 45.280 26.470 90.00 104.70 90.00 C 1 2 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 0.024468 0.000000 0.006419 0.00000
SCALE2 0.000000 0.022085 0.000000 0.00000
SCALE3 0.000000 0.000000 0.039057 0.00000
(ATOM LINES ARE NOT SHOWN.)
END