HEADER IRON-SULFUR PROTEIN 19-MAR-98 1A70 TITLE SPINACH FERREDOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPINACIA OLERACEA; SOURCE 3 ORGANISM_COMMON: SPINACH; SOURCE 4 ORGANISM_TAXID: 3562; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IRON-SULFUR PROTEIN, PHOTOSYNTHESIS, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.BINDA,A.CODA,A.MATTEVI,A.ALIVERTI,G.ZANETTI REVDAT 6 22-MAY-24 1A70 1 REMARK REVDAT 5 02-AUG-23 1A70 1 REMARK REVDAT 4 03-NOV-21 1A70 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1A70 1 VERSN REVDAT 2 13-JAN-99 1A70 3 ATOM SOURCE COMPND REMARK REVDAT 2 2 3 HETATM JRNL KEYWDS TER REVDAT 2 3 3 CONECT REVDAT 1 25-NOV-98 1A70 0 JRNL AUTH C.BINDA,A.CODA,A.ALIVERTI,G.ZANETTI,A.MATTEVI JRNL TITL STRUCTURE OF THE MUTANT E92K OF [2FE-2S] FERREDOXIN I FROM JRNL TITL 2 SPINACIA OLERACEA AT 1.7 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 54 1353 1998 JRNL REFN ISSN 0907-4449 JRNL PMID 10089511 JRNL DOI 10.1107/S0907444998005137 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5D REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 11755 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : A POSTERIORI REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY 10TH REFLECTION REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1090 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2010 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1960 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1176 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11755 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 : 81 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 5.100 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.019 ; 70.000; 620 REMARK 3 BOND ANGLES (DEGREES) : 2.994 ; 90.000; 855 REMARK 3 TORSION ANGLES (DEGREES) : 18.500; 0.000 ; 300 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.021 ; 70.000; 13 REMARK 3 GENERAL PLANES (A) : 0.021 ; 240.00; 94 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 4.300 ; 2.100 ; 620 REMARK 3 NON-BONDED CONTACTS (A) : 0.039 ; 125.00; 9 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BABINET SCALING REMARK 3 KSOL : 0.80 REMARK 3 BSOL : 150.0 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL V1.0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A70 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_1000170471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AGROVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11755 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.11200 REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.20200 REMARK 200 R SYM FOR SHELL (I) : 0.30500 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FRR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 2.6M REMARK 280 AMMONIUM SULPHATE IN 50MM PHOSPHATE BUFFER, PH 7.5 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 15.50000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.76000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.59000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.76000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.50000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.59000 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 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 ASP A 20 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 34 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 34 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP A 59 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 65 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 84 CB - CG - OD1 ANGL. DEV. = 12.2 DEGREES REMARK 500 ASP A 84 CB - CG - OD2 ANGL. DEV. = -14.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 SER A 38 -77.42 -141.70 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 FES A1602 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 39 SG REMARK 620 2 FES A1602 S1 116.8 REMARK 620 3 FES A1602 S2 100.8 104.5 REMARK 620 4 CYS A 44 SG 107.2 108.3 119.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A1602 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 47 SG REMARK 620 2 FES A1602 S1 113.0 REMARK 620 3 FES A1602 S2 109.6 105.4 REMARK 620 4 CYS A 77 SG 107.1 122.0 98.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 1602 DBREF 1A70 A 1 97 UNP P00221 FER1_SPIOL 51 147 SEQADV 1A70 LYS A 92 UNP P00221 GLU 142 ENGINEERED MUTATION SEQRES 1 A 97 ALA ALA TYR LYS VAL THR LEU VAL THR PRO THR GLY ASN SEQRES 2 A 97 VAL GLU PHE GLN CYS PRO ASP ASP VAL TYR ILE LEU ASP SEQRES 3 A 97 ALA ALA GLU GLU GLU GLY ILE ASP LEU PRO TYR SER CYS SEQRES 4 A 97 ARG ALA GLY SER CYS SER SER CYS ALA GLY LYS LEU LYS SEQRES 5 A 97 THR GLY SER LEU ASN GLN ASP ASP GLN SER PHE LEU ASP SEQRES 6 A 97 ASP ASP GLN ILE ASP GLU GLY TRP VAL LEU THR CYS ALA SEQRES 7 A 97 ALA TYR PRO VAL SER ASP VAL THR ILE GLU THR HIS LYS SEQRES 8 A 97 LYS GLU GLU LEU THR ALA HET FES A1602 4 HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 2 FES FE2 S2 FORMUL 3 HOH *81(H2 O) HELIX 1 1 ILE A 24 GLU A 30 1 7 HELIX 2 2 ASP A 66 GLU A 71 1 6 HELIX 3 3 THR A 76 ALA A 78 5 3 HELIX 4 4 LYS A 92 GLU A 94 5 3 SHEET 1 A 5 GLY A 12 PRO A 19 0 SHEET 2 A 5 ALA A 2 THR A 9 -1 N THR A 9 O GLY A 12 SHEET 3 A 5 VAL A 85 GLU A 88 1 N VAL A 85 O THR A 6 SHEET 4 A 5 ALA A 48 THR A 53 -1 N THR A 53 O THR A 86 SHEET 5 A 5 TRP A 73 LEU A 75 -1 N VAL A 74 O GLY A 49 LINK SG CYS A 39 FE1 FES A1602 1555 1555 2.32 LINK SG CYS A 44 FE1 FES A1602 1555 1555 2.28 LINK SG CYS A 47 FE2 FES A1602 1555 1555 2.36 LINK SG CYS A 77 FE2 FES A1602 1555 1555 2.27 SITE 1 AC1 8 SER A 38 CYS A 39 ARG A 40 GLY A 42 SITE 2 AC1 8 SER A 43 CYS A 44 CYS A 47 CYS A 77 CRYST1 31.000 39.180 83.520 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 0.032258 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011973 0.00000