HEADER OXIDOREDUCTASE 28-MAR-98 1A8P TITLE FERREDOXIN REDUCTASE FROM AZOTOBACTER VINELANDII COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADPH\:FERREDOXIN OXIDOREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FERREDOXIN REDUCTASE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII; SOURCE 3 ORGANISM_TAXID: 354; SOURCE 4 STRAIN: LM100 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR G.S.PRASAD,N.KRESGE,A.B.MUHLBERG,A.SHAW,Y.S.JUNG,B.K.BURGESS, AUTHOR 2 C.D.STOUT REVDAT 4 07-FEB-24 1A8P 1 REMARK REVDAT 3 04-APR-18 1A8P 1 REMARK REVDAT 2 24-FEB-09 1A8P 1 VERSN REVDAT 1 17-JUN-98 1A8P 0 JRNL AUTH G.SRIDHAR PRASAD,N.KRESGE,A.B.MUHLBERG,A.SHAW,Y.S.JUNG, JRNL AUTH 2 B.K.BURGESS,C.D.STOUT JRNL TITL THE CRYSTAL STRUCTURE OF NADPH:FERREDOXIN REDUCTASE FROM JRNL TITL 2 AZOTOBACTER VINELANDII. JRNL REF PROTEIN SCI. V. 7 2541 1998 JRNL REFN ISSN 0961-8368 JRNL PMID 9865948 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 18205 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 906 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 : 2061 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.60 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.530 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.290 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 1A8P 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_1000170532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-95 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 5.5 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 : MACSCIENCE REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (ROTAVATA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19076 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 34.18000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.33000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.18000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.33000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 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 ASN A 3 53.08 -93.05 REMARK 500 GLU A 62 47.98 -94.34 REMARK 500 GLU A 158 -62.95 -95.00 REMARK 500 PHE A 166 22.69 -158.54 REMARK 500 PRO A 211 8.00 -68.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 259 DBREF 1A8P A 2 258 UNP Q44532 FENR_AZOVI 1 257 SEQRES 1 A 258 MET SER ASN LEU ASN VAL GLU ARG VAL LEU SER VAL HIS SEQRES 2 A 258 HIS TRP ASN ASP THR LEU PHE SER PHE LYS THR THR ARG SEQRES 3 A 258 ASN PRO SER LEU ARG PHE GLU ASN GLY GLN PHE VAL MET SEQRES 4 A 258 ILE GLY LEU GLU VAL ASP GLY ARG PRO LEU MET ARG ALA SEQRES 5 A 258 TYR SER ILE ALA SER PRO ASN TYR GLU GLU HIS LEU GLU SEQRES 6 A 258 PHE PHE SER ILE LYS VAL GLN ASN GLY PRO LEU THR SER SEQRES 7 A 258 ARG LEU GLN HIS LEU LYS GLU GLY ASP GLU LEU MET VAL SEQRES 8 A 258 SER ARG LYS PRO THR GLY THR LEU VAL THR SER ASP LEU SEQRES 9 A 258 LEU PRO GLY LYS HIS LEU TYR MET LEU SER THR GLY THR SEQRES 10 A 258 GLY LEU ALA PRO PHE MET SER LEU ILE GLN ASP PRO GLU SEQRES 11 A 258 VAL TYR GLU ARG PHE GLU LYS VAL VAL LEU ILE HIS GLY SEQRES 12 A 258 VAL ARG GLN VAL ASN GLU LEU ALA TYR GLN GLN PHE ILE SEQRES 13 A 258 THR GLU HIS LEU PRO GLN SER GLU TYR PHE GLY GLU ALA SEQRES 14 A 258 VAL LYS GLU LYS LEU ILE TYR TYR PRO THR VAL THR ARG SEQRES 15 A 258 GLU SER PHE HIS ASN GLN GLY ARG LEU THR ASP LEU MET SEQRES 16 A 258 ARG SER GLY LYS LEU PHE GLU ASP ILE GLY LEU PRO PRO SEQRES 17 A 258 ILE ASN PRO GLN ASP ASP ARG ALA MET ILE CYS GLY SER SEQRES 18 A 258 PRO SER MET LEU ASP GLU SER CYS GLU VAL LEU ASP GLY SEQRES 19 A 258 PHE GLY LEU LYS ILE SER PRO ARG MET GLY GLU PRO GLY SEQRES 20 A 258 ASP TYR LEU ILE GLU ARG ALA PHE VAL GLU LYS HET FAD A 259 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 HOH *85(H2 O) HELIX 1 1 THR A 77 HIS A 82 1 6 HELIX 2 2 THR A 101 ASP A 103 5 3 HELIX 3 3 GLY A 116 LEU A 125 5 10 HELIX 4 4 PRO A 129 ARG A 134 1 6 HELIX 5 5 VAL A 147 GLU A 149 5 3 HELIX 6 6 GLN A 153 THR A 157 1 5 HELIX 7 7 HIS A 159 GLN A 162 1 4 HELIX 8 8 GLY A 167 LYS A 173 1 7 HELIX 9 9 LEU A 191 ARG A 196 1 6 HELIX 10 10 LYS A 199 ILE A 204 1 6 HELIX 11 11 PRO A 222 PHE A 235 1 14 SHEET 1 A 2 LEU A 4 ARG A 8 0 SHEET 2 A 2 GLU A 88 SER A 92 -1 N VAL A 91 O ASN A 5 SHEET 1 B 3 HIS A 63 ILE A 69 0 SHEET 2 B 3 LEU A 19 THR A 25 -1 N THR A 24 O LEU A 64 SHEET 3 B 3 VAL A 9 HIS A 14 -1 N HIS A 13 O SER A 21 SHEET 1 C 2 PHE A 37 VAL A 44 0 SHEET 2 C 2 ARG A 47 SER A 54 -1 N TYR A 53 O VAL A 38 SHEET 1 D 5 TYR A 249 ARG A 253 0 SHEET 2 D 5 ASP A 214 GLY A 220 1 N ALA A 216 O LEU A 250 SHEET 3 D 5 HIS A 109 THR A 115 1 N HIS A 109 O ARG A 215 SHEET 4 D 5 LYS A 137 VAL A 144 1 N LYS A 137 O LEU A 110 SHEET 5 D 5 LEU A 174 VAL A 180 1 N ILE A 175 O VAL A 138 CISPEP 1 GLY A 74 PRO A 75 0 -0.06 SITE 1 AC1 22 PHE A 37 ARG A 51 ALA A 52 TYR A 53 SITE 2 AC1 22 SER A 54 PHE A 67 ILE A 69 VAL A 71 SITE 3 AC1 22 GLY A 74 PRO A 75 LEU A 76 THR A 77 SITE 4 AC1 22 THR A 117 ALA A 120 ARG A 253 ALA A 254 SITE 5 AC1 22 PHE A 255 VAL A 256 LYS A 258 HOH A 268 SITE 6 AC1 22 HOH A 286 HOH A 316 CRYST1 68.360 76.660 52.040 90.00 90.00 90.00 P 21 21 2 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 0.014628 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019216 0.00000