HEADER ELECTRON TRANSPORT 11-DEC-98 7FD1 TITLE 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT PH 8.5, 100 K, 1.35 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (7-FE FERREDOXIN I); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FD1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII; SOURCE 3 ORGANISM_TAXID: 354 KEYWDS ELECTRON TRANSPORT, IRON-SULFUR EXPDTA X-RAY DIFFRACTION AUTHOR C.D.STOUT,E.A.STURA,D.E.MCREE REVDAT 7 20-SEP-23 7FD1 1 COMPND REMARK HETNAM LINK REVDAT 7 2 1 ATOM REVDAT 6 04-APR-18 7FD1 1 COMPND REMARK HETNAM ATOM REVDAT 5 04-OCT-17 7FD1 1 REMARK REVDAT 4 24-FEB-09 7FD1 1 VERSN REVDAT 3 22-DEC-99 7FD1 4 HEADER COMPND REMARK JRNL REVDAT 3 2 4 ATOM SOURCE SEQRES REVDAT 2 21-OCT-99 7FD1 3 DBREF ATOM REVDAT 1 16-DEC-98 7FD1 0 JRNL AUTH C.G.SCHIPKE,D.B.GOODIN,D.E.MCREE,C.D.STOUT JRNL TITL OXIDIZED AND REDUCED AZOTOBACTER VINELANDII FERREDOXIN I AT JRNL TITL 2 1.4 A RESOLUTION: CONFORMATIONAL CHANGE OF SURFACE RESIDUES JRNL TITL 3 WITHOUT SIGNIFICANT CHANGE IN THE [3FE-4S]+/0 CLUSTER. JRNL REF BIOCHEMISTRY V. 38 8228 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10387068 JRNL DOI 10.1021/BI983008I 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) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.158 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) : 28183 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)) : 0.136 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21624 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 841 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 993.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 771.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9067 REMARK 3 NUMBER OF RESTRAINTS : 10768 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.390 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.131 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.124 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.017 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.014 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.098 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.146 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: FE CLUSTERS NOT RESTRAINED REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7FD1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-98. REMARK 100 THE DEPOSITION ID IS D_1000000253. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 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 : MACSCIENCE REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS HI-STAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29311 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 200 DATA REDUNDANCY : 3.450 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34000 REMARK 200 FOR SHELL : 0.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: TRIVIAL CASE REMARK 200 STARTING MODEL: PDB ENTRY 6FD1 REMARK 200 REMARK 200 REMARK: ALL DATA INCLUDING NEGATIVE I'S WERE USED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CRYSTALLIZED FROM 60% SAT. REMARK 280 AMMONIUM SULFATE, 0.4M TRIS-HCL, PH 7.8 THE CRYSTALS WERE SOAKED REMARK 280 IN 0.15M TRIS/HCL PH 8.5 BEFORE DATA COLLECTION. STARTING MODEL REMARK 280 IN THE REFINEMENT WAS PDB ENTRY 6FD1. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 46.32500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.23000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.23000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.16250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.23000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.23000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.48750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.23000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.23000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.16250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.23000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.23000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.48750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 46.32500 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 ARG A 106 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = -4.2 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 108 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 F3S A 108 S1 120.9 REMARK 620 3 F3S A 108 S2 49.3 111.7 REMARK 620 4 F3S A 108 S3 54.5 105.6 103.7 REMARK 620 5 CYS A 49 SG 125.7 113.4 111.8 110.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A 108 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 F3S A 108 S2 108.8 REMARK 620 3 F3S A 108 S3 116.8 104.0 REMARK 620 4 F3S A 108 S4 112.9 110.6 103.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A 108 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 16 SG REMARK 620 2 F3S A 108 S1 107.1 REMARK 620 3 F3S A 108 S3 117.2 105.2 REMARK 620 4 F3S A 108 S4 114.7 111.3 100.9 REMARK 620 5 CYS A 49 SG 127.1 52.8 52.4 118.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 107 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 20 SG REMARK 620 2 SF4 A 107 S2 108.4 REMARK 620 3 SF4 A 107 S3 122.0 103.0 REMARK 620 4 SF4 A 107 S4 113.1 104.0 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 107 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 39 SG REMARK 620 2 SF4 A 107 S1 103.3 REMARK 620 3 SF4 A 107 S3 120.3 104.6 REMARK 620 4 SF4 A 107 S4 118.2 103.2 105.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 107 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 42 SG REMARK 620 2 SF4 A 107 S1 121.1 REMARK 620 3 SF4 A 107 S2 100.9 103.8 REMARK 620 4 SF4 A 107 S4 118.8 103.7 106.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 107 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 45 SG REMARK 620 2 SF4 A 107 S1 111.6 REMARK 620 3 SF4 A 107 S2 111.4 104.8 REMARK 620 4 SF4 A 107 S3 119.6 104.4 103.8 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 SF4 A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F3S A 108 DBREF 7FD1 A 1 106 UNP P00214 FER1_AZOVI 1 106 SEQRES 1 A 106 ALA PHE VAL VAL THR ASP ASN CYS ILE LYS CYS LYS TYR SEQRES 2 A 106 THR ASP CYS VAL GLU VAL CYS PRO VAL ASP CYS PHE TYR SEQRES 3 A 106 GLU GLY PRO ASN PHE LEU VAL ILE HIS PRO ASP GLU CYS SEQRES 4 A 106 ILE ASP CYS ALA LEU CYS GLU PRO GLU CYS PRO ALA GLN SEQRES 5 A 106 ALA ILE PHE SER GLU ASP GLU VAL PRO GLU ASP MET GLN SEQRES 6 A 106 GLU PHE ILE GLN LEU ASN ALA GLU LEU ALA GLU VAL TRP SEQRES 7 A 106 PRO ASN ILE THR GLU LYS LYS ASP PRO LEU PRO ASP ALA SEQRES 8 A 106 GLU ASP TRP ASP GLY VAL LYS GLY LYS LEU GLN HIS LEU SEQRES 9 A 106 GLU ARG HET SF4 A 107 8 HET F3S A 108 7 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM F3S FE3-S4 CLUSTER FORMUL 2 SF4 FE4 S4 FORMUL 3 F3S FE3 S4 FORMUL 4 HOH *138(H2 O) HELIX 1 1 ASP A 6 CYS A 8 5 3 HELIX 2 2 ASP A 15 VAL A 19 5 5 HELIX 3 3 GLU A 46 GLU A 48 5 3 HELIX 4 4 GLU A 57 GLU A 59 5 3 HELIX 5 5 GLU A 62 GLU A 76 5 15 HELIX 6 6 ALA A 91 TRP A 94 1 4 HELIX 7 7 LYS A 100 HIS A 103 5 4 SHEET 1 A 2 PHE A 2 VAL A 4 0 SHEET 2 A 2 ILE A 54 SER A 56 -1 N PHE A 55 O VAL A 3 SHEET 1 B 2 PHE A 25 GLU A 27 0 SHEET 2 B 2 LEU A 32 ILE A 34 -1 N VAL A 33 O TYR A 26 LINK SG CYS A 8 FE1 F3S A 108 1555 1555 4.67 LINK SG CYS A 8 FE4 F3S A 108 1555 1555 2.24 LINK SG CYS A 16 FE3 F3S A 108 1555 1555 2.26 LINK SG CYS A 20 FE1 SF4 A 107 1555 1555 2.30 LINK SG CYS A 39 FE2 SF4 A 107 1555 1555 2.30 LINK SG CYS A 42 FE3 SF4 A 107 1555 1555 2.21 LINK SG CYS A 45 FE4 SF4 A 107 1555 1555 2.25 LINK SG CYS A 49 FE3 F3S A 108 1555 1555 4.67 LINK SG CYS A 49 FE1 F3S A 108 1555 1555 2.27 SITE 1 AC1 10 PHE A 2 CYS A 20 VAL A 22 CYS A 24 SITE 2 AC1 10 PHE A 25 CYS A 39 ILE A 40 CYS A 42 SITE 3 AC1 10 ALA A 43 CYS A 45 SITE 1 AC2 8 VAL A 4 CYS A 8 LYS A 12 TYR A 13 SITE 2 AC2 8 THR A 14 ASP A 15 CYS A 16 CYS A 49 CRYST1 54.460 54.460 92.650 90.00 90.00 90.00 P 41 21 2 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 0.018362 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010793 0.00000