HEADER ELECTRON TRANSPORT 07-DEC-81 3FXC OBSLTE 07-DEC-95 3FXC 4FXC TITLE X-*RAY ANALYSIS OF A (2*FE-2*S) FERREDOXIN FROM SPIRULINA TITLE 2 $PLATENSIS. MAIN CHAIN FOLD AND LOCATION OF SIDE CHAINS AT TITLE 3 2.5 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.KAKUDO,T.TSUKIHARA,Y.KATSUBE REVDAT 5 22-OCT-84 3FXC 1 SEQRES REVDAT 4 17-FEB-84 3FXC 3 HETATM REVDAT 3 31-JAN-84 3FXC 1 REMARK REVDAT 2 30-SEP-83 3FXC 1 REVDAT REVDAT 1 03-FEB-82 3FXC 0 SPRSDE 03-FEB-82 3FXC 1FXC JRNL AUTH T.TSUKIHARA,K.FUKUYAMA,M.NAKAMURA,Y.KATSUBE, JRNL AUTH 2 N.TANAKA,M.KAKUDO,K.WADA,T.HASE,H.MATSUBARA JRNL TITL X-RAY ANALYSIS OF A (2FE-2S) FERREDOXIN FROM JRNL TITL 2 SPIRULINA PLATENSIS. MAIN CHAIN FOLD AND LOCATION JRNL TITL 3 OF SIDE CHAINS AT 2.5 ANGSTROMS RESOLUTION JRNL REF J.BIOCHEM.(TOKYO) V. 90 1763 1981 JRNL REFN ASTM JOBIAO JA ISSN 0021-924X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.FUKUYAMA,T.HASE,S.MATSUMOTO,T.TSUKIHARA, REMARK 1 AUTH 2 Y.KATSUBE,N.TANAKA,M.KAKUDO,K.WADA,H.MATSUBARA REMARK 1 TITL STRUCTURE OF S. PLATENSIS (2FE-2S) FERREDOXIN AND REMARK 1 TITL 2 EVOLUTION OF CHLOROPLAST-TYPE FERREDOXINS REMARK 1 REF NATURE V. 286 522 1980 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.TSUKIHARA,K.FUKUYAMA,H.TAHARA,Y.KATSUBE, REMARK 1 AUTH 2 Y.MATSUURA,N.TANAKA,M.KAKUDO,K.WADA,H.MATSUBARA REMARK 1 TITL X-RAY ANALYSIS OF FERREDOXIN FROM SPIRULINA REMARK 1 TITL 2 PLATENSIS. /II. CHELATE STRUCTURE OF ACTIVE CENTER REMARK 1 REF J.BIOCHEM.(TOKYO) V. 84 1645 1978 REMARK 1 REFN ASTM JOBIAO JA ISSN 0021-924X REMARK 1 REFERENCE 3 REMARK 1 AUTH K.OGAWA,T.TSUKIHARA,H.TAHARA,Y.KATSUBE,Y.MATSU-URA, REMARK 1 AUTH 2 N.TANAKA,M.KAKUDO,K.WADA,H.MATSUBARA REMARK 1 TITL LOCATION OF THE IRON-SULFUR CLUSTER IN SPIRULINA REMARK 1 TITL 2 PLATENSIS FERREDOXIN BY X-RAY ANALYSIS REMARK 1 REF J.BIOCHEM.(TOKYO) V. 81 529 1977 REMARK 1 REFN ASTM JOBIAO JA ISSN 0021-924X REMARK 1 REFERENCE 4 REMARK 1 EDIT M.O.DAYHOFF REMARK 1 REF ATLAS OF PROTEIN SEQUENCE V. 5 54 1978 REMARK 1 REF 2 AND STRUCTURE,SUPPLEMENT 3 REMARK 1 PUBL NATIONAL BIOMEDICAL RESEARCH FOUNDATION, SILVER REMARK 1 PUBL 2 SPRING,MD. REMARK 1 REFN ISSN 0-912466-07-3 REMARK 2 REMARK 2 RESOLUTION. NULL ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL 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 : 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 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 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 : 732 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 0 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 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 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 3FXC COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 3FXC CORRECTION. CORRECT JOURNAL NAME FOR REFERENCES 1, 3, REMARK 5 4. 3FXC 31-JAN-84. 3FXC REMARK 6 REMARK 6 3FXC CORRECTION. CORRECT ATOM NAME FOR FE1 AND FE2 IN FES REMARK 6 3FXC GROUP. 17-FEB-84. 3FXC REMARK 7 REMARK 7 3FXC CORRECTION. CORRECT SEQRES RECORD. 22-OCT-84. 3FXC 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 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 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 (%): 46.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 3555 -X,Y,1/2-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 1/2+X,1/2+Y,Z REMARK 290 6555 1/2-X,1/2-Y,1/2+Z REMARK 290 7555 1/2-X,1/2+Y,1/2-Z REMARK 290 8555 1/2+X,1/2-Y,-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 -54.04237 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 -54.04237 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 -31.16041 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 14.25517 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 -31.16041 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 14.25517 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 -54.04237 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 -31.16041 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 14.25517 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 -54.04237 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 -31.16041 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 14.25517 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O GLU 31 N GLY 34 2.00 REMARK 500 OG1 THR 57 OD1 ASP 59 2.01 REMARK 500 O ASN 9 N ALA 11 2.12 REMARK 500 O GLU 31 CA GLY 34 2.13 REMARK 500 O VAL 5 N ILE 18 2.18 REMARK 500 CG GLN 60 OG1 THR 84 2.18 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 N GLU 94 C GLU 94 4555 1.01 REMARK 500 OH TYR 39 OE2 GLU 72 5455 1.07 REMARK 500 CA LEU 97 CA LEU 97 4555 1.42 REMARK 500 CA GLU 94 C GLU 94 4555 1.44 REMARK 500 N GLU 94 O GLU 94 4555 1.73 REMARK 500 OH TYR 75 N LEU 97 4555 1.89 REMARK 500 CB ALA 45 CG2 THR 54 1565 1.90 REMARK 500 C GLU 94 C GLU 94 4555 1.93 REMARK 500 O ALA 43 CB SER 55 1565 1.99 REMARK 500 C GLN 93 CA GLU 95 4555 2.02 REMARK 500 O ALA 50 CG GLU 95 4555 2.03 REMARK 500 CA LEU 97 CB LEU 97 4555 2.17 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN 60 CA - CB - CG ANGL. DEV. = 64.5 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 CYS 41 -81.71 138.07 REMARK 500 SER 55 -119.38 12.31 REMARK 500 ASP 67 127.38 129.16 REMARK 500 TYR 75 79.59 119.46 SEQRES 1 98 ALA THR TYR LYS VAL THR LEU ILE ASN GLU ALA GLU GLY SEQRES 2 98 ILE ASN GLU THR ILE ASP CYS ASP ASP ASP THR TYR ILE SEQRES 3 98 LEU ASP ALA ALA GLU GLU ALA GLY LEU ASP LEU PRO TYR SEQRES 4 98 SER CYS ARG ALA GLY ALA CYS SER THR CYS ALA GLY THR SEQRES 5 98 ILE THR SER GLY THR ILE ASP GLN SER ASP GLN SER PHE SEQRES 6 98 LEU ASP ASP ASP GLN ILE GLU ALA GLY TYR VAL LEU THR SEQRES 7 98 CYS VAL ALA TYR PRO THR SER ASP CYS THR ILE LYS THR SEQRES 8 98 HIS GLN GLU GLU GLY LEU TYR HET FES 1 4 HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 2 FES FE2 S2 HELIX 1 H1 TYR 25 GLY 34 1 10 SHEET 1 A 3 ASN 15 CYS 20 0 SHEET 2 A 3 TYR 3 ILE 8 -1 N VAL 5 O ILE 18 SHEET 3 A 3 CYS 87 ILE 89 1 O ILE 89 N THR 6 SSBOND 1 CYS 49 CYS 79 CRYST1 62.320 28.510 108.080 90.00 90.00 90.00 C 2 2 21 8 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 -0.016046 0.000000 0.000000 0.25000 SCALE2 0.000000 0.035075 0.000000 0.18900 SCALE3 0.000000 0.000000 -0.009252 0.25000