HEADER FLAVOPROTEIN 06-MAR-97 1FDR TITLE FLAVODOXIN REDUCTASE FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVODOXIN REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FERREDOXIN REDUCTASE; COMPND 5 EC: 1.18.1.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: K12 C600; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: FPR; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: S30; SOURCE 10 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PEE1010 KEYWDS FLAVODOXIN REDUCTASE, FERREDOXIN REDUCTASE, FLAVIN, OXIDOREDUCTASE, KEYWDS 2 FLAVOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.INGELMAN,V.BIANCHI,H.EKLUND REVDAT 4 07-FEB-24 1FDR 1 REMARK REVDAT 3 03-NOV-21 1FDR 1 REMARK SEQADV REVDAT 2 24-FEB-09 1FDR 1 VERSN REVDAT 1 17-SEP-97 1FDR 0 JRNL AUTH M.INGELMAN,V.BIANCHI,H.EKLUND JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF FLAVODOXIN REDUCTASE FROM JRNL TITL 2 ESCHERICHIA COLI AT 1.7 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 268 147 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9149148 JRNL DOI 10.1006/JMBI.1997.0957 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19171 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) : 0.184 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 30.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1200 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.00 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 : 1920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.10 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.980 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.500 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FDR 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_1000173250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-94 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 7.3 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 : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28503 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 17.8000 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) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 29.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23000 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M SODIUM CITRATE 100MM TRISHCL PH REMARK 280 7.3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 62.06500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.06500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.55000 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 465 ASP A 44 REMARK 465 GLY A 45 REMARK 465 GLU A 46 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 105 CG ND1 CD2 CE1 NE2 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 O HOH A 293 O HOH A 410 4546 0.77 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 ARG A 238 84.40 -166.37 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 249 DBREF 1FDR A 2 248 UNP P28861 FENR_ECOLI 1 247 SEQADV 1FDR ARG A 126 UNP P28861 GLN 125 ENGINEERED MUTATION SEQRES 1 A 248 MET ALA ASP TRP VAL THR GLY LYS VAL THR LYS VAL GLN SEQRES 2 A 248 ASN TRP THR ASP ALA LEU PHE SER LEU THR VAL HIS ALA SEQRES 3 A 248 PRO VAL LEU PRO PHE THR ALA GLY GLN PHE THR LYS LEU SEQRES 4 A 248 GLY LEU GLU ILE ASP GLY GLU ARG VAL GLN ARG ALA TYR SEQRES 5 A 248 SER TYR VAL ASN SER PRO ASP ASN PRO ASP LEU GLU PHE SEQRES 6 A 248 TYR LEU VAL THR VAL PRO ASP GLY LYS LEU SER PRO ARG SEQRES 7 A 248 LEU ALA ALA LEU LYS PRO GLY ASP GLU VAL GLN VAL VAL SEQRES 8 A 248 SER GLU ALA ALA GLY PHE PHE VAL LEU ASP GLU VAL PRO SEQRES 9 A 248 HIS CYS GLU THR LEU TRP MET LEU ALA THR GLY THR ALA SEQRES 10 A 248 ILE GLY PRO TYR LEU SER ILE LEU ARG LEU GLY LYS ASP SEQRES 11 A 248 LEU ASP ARG PHE LYS ASN LEU VAL LEU VAL HIS ALA ALA SEQRES 12 A 248 ARG TYR ALA ALA ASP LEU SER TYR LEU PRO LEU MET GLN SEQRES 13 A 248 GLU LEU GLU LYS ARG TYR GLU GLY LYS LEU ARG ILE GLN SEQRES 14 A 248 THR VAL VAL SER ARG GLU THR ALA ALA GLY SER LEU THR SEQRES 15 A 248 GLY ARG ILE PRO ALA LEU ILE GLU SER GLY GLU LEU GLU SEQRES 16 A 248 SER THR ILE GLY LEU PRO MET ASN LYS GLU THR SER HIS SEQRES 17 A 248 VAL MET LEU CYS GLY ASN PRO GLN MET VAL ARG ASP THR SEQRES 18 A 248 GLN GLN LEU LEU LYS GLU THR ARG GLN MET THR LYS HIS SEQRES 19 A 248 LEU ARG ARG ARG PRO GLY HIS MET THR ALA GLU HIS TYR SEQRES 20 A 248 TRP HET FAD A 249 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 HOH *205(H2 O) HELIX 1 1 SER A 76 ALA A 81 1 6 HELIX 2 2 LEU A 100 GLU A 102 5 3 HELIX 3 3 GLY A 115 LEU A 127 5 13 HELIX 4 4 ALA A 146 ASP A 148 5 3 HELIX 5 5 LEU A 152 ARG A 161 1 10 HELIX 6 6 ILE A 185 GLU A 190 1 6 HELIX 7 7 GLU A 193 ILE A 198 1 6 HELIX 8 8 PRO A 215 ARG A 229 1 15 SHEET 1 A 4 GLU A 87 VAL A 91 0 SHEET 2 A 4 TRP A 4 ASN A 14 -1 N GLY A 7 O VAL A 88 SHEET 3 A 4 LEU A 19 ALA A 26 -1 N HIS A 25 O LYS A 8 SHEET 4 A 4 LEU A 63 VAL A 68 -1 N LEU A 67 O PHE A 20 SHEET 1 B 2 PHE A 36 LEU A 41 0 SHEET 2 B 2 VAL A 48 SER A 53 -1 N TYR A 52 O THR A 37 SHEET 1 C 6 MET A 242 HIS A 246 0 SHEET 2 C 6 SER A 207 GLY A 213 1 N VAL A 209 O THR A 243 SHEET 3 C 6 THR A 108 THR A 114 1 N THR A 108 O HIS A 208 SHEET 4 C 6 ASN A 136 ALA A 143 1 N ASN A 136 O LEU A 109 SHEET 5 C 6 LEU A 166 VAL A 172 1 N ARG A 167 O LEU A 137 SHEET 6 C 6 SER A 180 THR A 182 1 N LEU A 181 O THR A 170 SITE 1 AC1 24 PHE A 36 ARG A 50 ALA A 51 TYR A 52 SITE 2 AC1 24 SER A 53 TYR A 66 LEU A 67 VAL A 68 SITE 3 AC1 24 VAL A 70 GLY A 73 LYS A 74 LEU A 75 SITE 4 AC1 24 SER A 76 THR A 116 HIS A 246 TYR A 247 SITE 5 AC1 24 TRP A 248 HOH A 269 HOH A 270 HOH A 271 SITE 6 AC1 24 HOH A 313 HOH A 330 HOH A 352 HOH A 383 CRYST1 124.130 51.100 40.670 90.00 93.10 90.00 C 1 2 1 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 0.008056 0.000000 0.000436 0.00000 SCALE2 0.000000 0.019569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024624 0.00000