HEADER ELECTRON TRANSPORT 01-JUL-99 1QT9 TITLE OXIDIZED [2FE-2S] FERREDOXIN FROM ANABAENA PCC7119 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN I; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC SP.; SOURCE 3 ORGANISM_TAXID: 1168; SOURCE 4 STRAIN: PCC 7119 KEYWDS OXIDIZED FERREDOXIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR R.MORALES,M.-H.CHRON,G.HUDRY-CLERGEON,Y.PETILLOT,S.NORAGER,M.MEDINA, AUTHOR 2 M.FREY REVDAT 8 16-AUG-23 1QT9 1 REMARK LINK REVDAT 7 11-APR-18 1QT9 1 REMARK REVDAT 6 04-APR-18 1QT9 1 REMARK REVDAT 5 13-JUL-11 1QT9 1 VERSN REVDAT 4 24-FEB-09 1QT9 1 VERSN REVDAT 3 01-APR-03 1QT9 1 JRNL REVDAT 2 26-JUN-00 1QT9 3 SOURCE HETATM REVDAT 1 02-DEC-99 1QT9 0 JRNL AUTH R.MORALES,M.H.CHARON,G.HUDRY-CLERGEON,Y.PETILLOT,S.NORAGER, JRNL AUTH 2 M.MEDINA,M.FREY JRNL TITL REFINED X-RAY STRUCTURES OF THE OXIDIZED, AT 1.3 A, AND JRNL TITL 2 REDUCED, AT 1.17 A, [2FE-2S] FERREDOXIN FROM THE JRNL TITL 3 CYANOBACTERIUM ANABAENA PCC7119 SHOW REDOX-LINKED JRNL TITL 4 CONFORMATIONAL CHANGES. JRNL REF BIOCHEMISTRY V. 38 15764 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10625442 JRNL DOI 10.1021/BI991578S REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.2 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) : 0.160 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.138 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2656 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 26254 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.133 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2404 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21461 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 750 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 968.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 686.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 809 REMARK 3 NUMBER OF RESTRAINTS : 959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.020 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.120 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.110 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.030 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.010 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.030 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.020 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: [2FE-2S] CLUSTERS NOT RESTRAINED REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, REMARK 3 J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) REMARK 3 BY 2.5 % REMARK 4 REMARK 4 1QT9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009273. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-97 REMARK 200 TEMPERATURE (KELVIN) : 100. REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27431 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.22600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM SODIUM SUCCINATE PH 5.5, 2.6 M REMARK 280 AMMONIUM SULFATE, 1% MPD AT 4 C, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 90.33333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.16667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.16667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.33333 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 GLU A 17 OE1 - CD - OE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP A 28 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 42 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 PHE A 65 CG - CD1 - CE1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 68 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 GLU A 72 OE1 - CD - OE2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 96 CB - CG - OD2 ANGL. DEV. = -5.8 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 40 -74.41 -139.95 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 A 999 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 41 SG REMARK 620 2 FES A 999 S1 119.9 REMARK 620 3 FES A 999 S2 102.2 102.5 REMARK 620 4 CYS A 46 SG 105.9 108.1 119.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 999 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 FES A 999 S1 112.4 REMARK 620 3 FES A 999 S2 111.2 105.6 REMARK 620 4 CYS A 79 SG 106.6 116.0 104.8 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 999 DBREF 1QT9 A 1 98 UNP P0A3C8 FER1_ANASO 2 99 SEQRES 1 A 98 ALA THR PHE LYS VAL THR LEU ILE ASN GLU ALA GLU GLY SEQRES 2 A 98 THR LYS HIS GLU ILE GLU VAL PRO ASP ASP GLU TYR ILE SEQRES 3 A 98 LEU ASP ALA ALA GLU GLU GLN GLY TYR ASP LEU PRO PHE SEQRES 4 A 98 SER CYS ARG ALA GLY ALA CYS SER THR CYS ALA GLY LYS SEQRES 5 A 98 LEU VAL SER GLY THR VAL ASP GLN SER ASP GLN SER PHE SEQRES 6 A 98 LEU ASP ASP ASP GLN ILE GLU ALA GLY TYR VAL LEU THR SEQRES 7 A 98 CYS VAL ALA TYR PRO THR SER ASP VAL VAL ILE GLN THR SEQRES 8 A 98 HIS LYS GLU GLU ASP LEU TYR HET FES A 999 4 HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 2 FES FE2 S2 FORMUL 3 HOH *238(H2 O) HELIX 1 1 TYR A 25 GLN A 33 1 9 HELIX 2 2 ASP A 67 ALA A 73 1 7 HELIX 3 3 CYS A 79 ALA A 81 5 3 HELIX 4 4 LYS A 93 LEU A 97 5 5 SHEET 1 A 5 THR A 14 PRO A 21 0 SHEET 2 A 5 THR A 2 ASN A 9 -1 O PHE A 3 N VAL A 20 SHEET 3 A 5 VAL A 87 GLN A 90 1 O VAL A 87 N THR A 6 SHEET 4 A 5 ALA A 50 SER A 55 -1 O LYS A 52 N GLN A 90 SHEET 5 A 5 TYR A 75 LEU A 77 -1 O VAL A 76 N GLY A 51 SHEET 1 B 2 VAL A 58 ASP A 59 0 SHEET 2 B 2 TYR A 82 PRO A 83 -1 O TYR A 82 N ASP A 59 LINK SG CYS A 41 FE1 FES A 999 1555 1555 2.34 LINK SG CYS A 46 FE1 FES A 999 1555 1555 2.28 LINK SG CYS A 49 FE2 FES A 999 1555 1555 2.29 LINK SG CYS A 79 FE2 FES A 999 1555 1555 2.29 SITE 1 AC1 9 SER A 40 CYS A 41 ARG A 42 GLY A 44 SITE 2 AC1 9 ALA A 45 CYS A 46 CYS A 49 LEU A 77 SITE 3 AC1 9 CYS A 79 CRYST1 37.400 37.400 135.500 90.00 90.00 120.00 P 32 2 1 6 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 0.026738 0.015437 0.000000 0.00000 SCALE2 0.000000 0.030874 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007380 0.00000