HEADER ELECTRON TRANSPORT 08-SEP-99 1D03 TITLE REFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS NIDULANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVODOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: OXIDIZED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS ELONGATUS; SOURCE 3 ORGANISM_TAXID: 1140; SOURCE 4 STRAIN: PCC 7942; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: W1485; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKK233-2-ANFLD KEYWDS FLAVODOXIN, FMN BINDING, REDOX POTENTIAL, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.L.DRENNAN,K.A.PATTRIDGE,C.H.WEBER,A.L.METZGER,D.M.HOOVER,M.L.LUDWIG REVDAT 6 07-FEB-24 1D03 1 REMARK REVDAT 5 03-NOV-21 1D03 1 REMARK SEQADV REVDAT 4 04-APR-18 1D03 1 REMARK REVDAT 3 13-JUL-11 1D03 1 VERSN REVDAT 2 24-FEB-09 1D03 1 VERSN REVDAT 1 29-DEC-99 1D03 0 JRNL AUTH C.L.DRENNAN,K.A.PATTRIDGE,C.H.WEBER,A.L.METZGER,D.M.HOOVER, JRNL AUTH 2 M.L.LUDWIG JRNL TITL REFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS JRNL TITL 2 NIDULANS. JRNL REF J.MOL.BIOL. V. 294 711 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10610791 JRNL DOI 10.1006/JMBI.1999.3151 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 21005 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : A POSTERIORI REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2092 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2873 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE : 0.2240 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 335 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1314 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 134 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.520 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.810 ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM.FMN REMARK 3 PARAMETER FILE 3 : PARAM.WAT REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH.FMN REMARK 3 TOPOLOGY FILE 3 : TOPH.WAT REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D03 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009666. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-91 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6.8 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SDMS REMARK 200 DATA SCALING SOFTWARE : SDMS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 68.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, POTASSIUM PHOSPHATE, REMARK 280 PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 25.65000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.22000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.57500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.22000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.65000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.57500 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: 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 VAL A 59 74.50 60.37 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 FMN A 170 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CZN RELATED DB: PDB REMARK 900 WILDTYPE FORM I OXIDIZED FLAVODOXIN REMARK 900 RELATED ID: 1CZU RELATED DB: PDB REMARK 900 WILDTYPE FORM II OXIDIZED FLAVODOXIN REMARK 900 RELATED ID: 1CZL RELATED DB: PDB REMARK 900 WILDTYPE SEMIQUINONE FLAVODOXIN REMARK 900 RELATED ID: 1D04 RELATED DB: PDB REMARK 900 WILDTYPE HYDROQUINONE FLAVODOXIN REMARK 900 RELATED ID: 1D03 RELATED DB: PDB REMARK 900 MUTANT N58G OXIDIZED FLAVODOXIN REMARK 900 RELATED ID: 1CZH RELATED DB: PDB REMARK 900 MUTANT N58G SEMIQUINONE FLAVODOXIN REMARK 900 RELATED ID: 1CZO RELATED DB: PDB REMARK 900 MUTANT N58G HYDROQUINONE FLAVODOXIN REMARK 900 RELATED ID: 1CZR RELATED DB: PDB REMARK 900 MUTANT D90N OXIDIZED FLAVODOXIN REMARK 900 RELATED ID: 1CZK RELATED DB: PDB REMARK 900 MUTANT D100N OXIDIZED FLAVODOXIN DBREF 1D03 A 1 169 UNP P10340 FLAV_SYNP7 1 169 SEQADV 1D03 GLY A 58 UNP P10340 ASN 58 ENGINEERED MUTATION SEQRES 1 A 169 ALA LYS ILE GLY LEU PHE TYR GLY THR GLN THR GLY VAL SEQRES 2 A 169 THR GLN THR ILE ALA GLU SER ILE GLN GLN GLU PHE GLY SEQRES 3 A 169 GLY GLU SER ILE VAL ASP LEU ASN ASP ILE ALA ASN ALA SEQRES 4 A 169 ASP ALA SER ASP LEU ASN ALA TYR ASP TYR LEU ILE ILE SEQRES 5 A 169 GLY CYS PRO THR TRP GLY VAL GLY GLU LEU GLN SER ASP SEQRES 6 A 169 TRP GLU GLY ILE TYR ASP ASP LEU ASP SER VAL ASN PHE SEQRES 7 A 169 GLN GLY LYS LYS VAL ALA TYR PHE GLY ALA GLY ASP GLN SEQRES 8 A 169 VAL GLY TYR SER ASP ASN PHE GLN ASP ALA MET GLY ILE SEQRES 9 A 169 LEU GLU GLU LYS ILE SER SER LEU GLY SER GLN THR VAL SEQRES 10 A 169 GLY TYR TRP PRO ILE GLU GLY TYR ASP PHE ASN GLU SER SEQRES 11 A 169 LYS ALA VAL ARG ASN ASN GLN PHE VAL GLY LEU ALA ILE SEQRES 12 A 169 ASP GLU ASP ASN GLN PRO ASP LEU THR LYS ASN ARG ILE SEQRES 13 A 169 LYS THR TRP VAL SER GLN LEU LYS SER GLU PHE GLY LEU HET FMN A 170 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 HOH *134(H2 O) HELIX 1 1 GLY A 12 GLY A 26 1 15 HELIX 2 2 ALA A 37 ALA A 39 5 3 HELIX 3 3 ASP A 40 TYR A 47 5 8 HELIX 4 4 GLN A 63 TYR A 70 1 8 HELIX 5 5 ASP A 71 VAL A 76 5 6 HELIX 6 6 GLN A 99 SER A 111 1 13 HELIX 7 7 GLN A 148 ASP A 150 5 3 HELIX 8 8 LEU A 151 PHE A 167 1 17 SHEET 1 A 5 VAL A 31 ASP A 35 0 SHEET 2 A 5 ILE A 3 TYR A 7 1 O ILE A 3 N ASP A 32 SHEET 3 A 5 TYR A 49 GLY A 53 1 O TYR A 49 N GLY A 4 SHEET 4 A 5 LYS A 82 ALA A 88 1 O LYS A 82 N LEU A 50 SHEET 5 A 5 GLN A 115 THR A 116 1 O GLN A 115 N VAL A 83 SHEET 1 A1 5 VAL A 31 ASP A 35 0 SHEET 2 A1 5 ILE A 3 TYR A 7 1 O ILE A 3 N ASP A 32 SHEET 3 A1 5 TYR A 49 GLY A 53 1 O TYR A 49 N GLY A 4 SHEET 4 A1 5 LYS A 82 ALA A 88 1 O LYS A 82 N LEU A 50 SHEET 5 A1 5 LEU A 141 ILE A 143 1 O LEU A 141 N GLY A 87 SHEET 1 B 2 THR A 56 TRP A 57 0 SHEET 2 B 2 GLU A 61 LEU A 62 -1 N GLU A 61 O TRP A 57 SHEET 1 C 3 TRP A 120 PRO A 121 0 SHEET 2 C 3 GLN A 137 PHE A 138 -1 N PHE A 138 O TRP A 120 SHEET 3 C 3 VAL A 133 ARG A 134 -1 N ARG A 134 O GLN A 137 SITE 1 AC1 23 THR A 9 GLN A 10 THR A 11 GLY A 12 SITE 2 AC1 23 VAL A 13 THR A 14 PRO A 55 THR A 56 SITE 3 AC1 23 TRP A 57 VAL A 59 GLY A 60 ASN A 77 SITE 4 AC1 23 ALA A 88 GLY A 89 ASP A 90 TYR A 94 SITE 5 AC1 23 ASN A 97 PHE A 98 GLN A 99 ASP A 146 SITE 6 AC1 23 HOH A 171 HOH A 172 HOH A 228 CRYST1 51.300 59.150 94.440 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 0.019493 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016906 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010589 0.00000