HEADER ELECTRON TRANSPORT 08-JUN-00 1F4P TITLE Y98W FLAVODOXIN MUTANT 1.5A (D. VULGARIS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVODOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 881; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ELECTRON TRANSPORT, FLAVOPROTEIN, FMN, 3D-STRCTURE, ANISOTROPIC KEYWDS 2 REFINEMENT, REDOX PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.A.REYNOLDS,W.WATT,K.D.WATENPAUGH REVDAT 6 07-FEB-24 1F4P 1 REMARK REVDAT 5 03-NOV-21 1F4P 1 SEQADV REVDAT 4 21-JUL-21 1F4P 1 REMARK REVDAT 3 04-OCT-17 1F4P 1 REMARK REVDAT 2 24-FEB-09 1F4P 1 VERSN REVDAT 1 04-APR-01 1F4P 0 JRNL AUTH R.A.REYNOLDS,W.WATT,K.D.WATENPAUGH JRNL TITL STRUCTURES AND COMPARISON OF THE Y98H (2.0 A) AND Y98W (1.5 JRNL TITL 2 A) MUTANTS OF FLAVODOXIN (DESULFOVIBRIO VULGARIS). JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 527 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11264581 JRNL DOI 10.1107/S0907444901002554 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) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.6 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY 75TH REFLECTION REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.126 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 336 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 31010 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)) : NULL 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)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1104 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 306 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 ANGLE DISTANCES (A) : 2.120 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ANISOTROPIC REFINEMENT, NO REMARK 3 CONSTRAINTS REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-91 REMARK 200 TEMPERATURE (KELVIN) : 291 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 : SIEMENS 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 : 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 : 31010 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.6 REMARK 200 DATA REDUNDANCY : 3.490 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.95 REMARK 200 R MERGE FOR SHELL (I) : 0.50700 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: MERLOT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS BUFFER, PH 7.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292.K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.91000 REMARK 290 SMTRY3 2 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 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 PRO A 2 CG CD 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 PRO A 2 N - CA - CB ANGL. DEV. = 10.2 DEGREES REMARK 500 ASP A 63 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 LEU A 67 CB - CG - CD2 ANGL. DEV. = 12.8 DEGREES REMARK 500 LEU A 78 CB - CG - CD1 ANGL. DEV. = 11.6 DEGREES REMARK 500 PHE A 101 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 PHE A 101 CB - CG - CD1 ANGL. DEV. = 4.7 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 ASP A 63 42.32 -148.58 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 149 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FX1 RELATED DB: PDB REMARK 900 STRUCTURE OF BASE FLAVODOXIN BEFORE MUTATION. REMARK 900 RELATED ID: 2FX2 RELATED DB: PDB REMARK 900 DIFFERENT OXIDATION STATES OF "NATIVE" USED IN COMPARISIONS TO REMARK 900 CURRENT STRUCTURE REMARK 900 RELATED ID: 3FX2 RELATED DB: PDB REMARK 900 DIFFERENT OXIDATION STATES OF "NATIVE" USED IN COMPARISIONS TO REMARK 900 CURRENT STRUCTURE REMARK 900 RELATED ID: 4FX2 RELATED DB: PDB REMARK 900 DIFFERENT OXIDATION STATES OF "NATIVE" USED IN COMPARISIONS TO REMARK 900 CURRENT STRUCTURE REMARK 900 RELATED ID: 5FX2 RELATED DB: PDB REMARK 900 DIFFERENT OXIDATION STATES OF "NATIVE" USED IN COMPARISIONS TO REMARK 900 CURRENT STRUCTURE DBREF 1F4P A 2 148 UNP P00323 FLAV_DESVH 2 148 SEQADV 1F4P TRP A 98 UNP P00323 TYR 98 ENGINEERED MUTATION SEQRES 1 A 147 PRO LYS ALA LEU ILE VAL TYR GLY SER THR THR GLY ASN SEQRES 2 A 147 THR GLU TYR THR ALA GLU THR ILE ALA ARG GLU LEU ALA SEQRES 3 A 147 ASP ALA GLY TYR GLU VAL ASP SER ARG ASP ALA ALA SER SEQRES 4 A 147 VAL GLU ALA GLY GLY LEU PHE GLU GLY PHE ASP LEU VAL SEQRES 5 A 147 LEU LEU GLY CYS SER THR TRP GLY ASP ASP SER ILE GLU SEQRES 6 A 147 LEU GLN ASP ASP PHE ILE PRO LEU PHE ASP SER LEU GLU SEQRES 7 A 147 GLU THR GLY ALA GLN GLY ARG LYS VAL ALA CYS PHE GLY SEQRES 8 A 147 CYS GLY ASP SER SER TRP GLU TYR PHE CYS GLY ALA VAL SEQRES 9 A 147 ASP ALA ILE GLU GLU LYS LEU LYS ASN LEU GLY ALA GLU SEQRES 10 A 147 ILE VAL GLN ASP GLY LEU ARG ILE ASP GLY ASP PRO ARG SEQRES 11 A 147 ALA ALA ARG ASP ASP ILE VAL GLY TRP ALA HIS ASP VAL SEQRES 12 A 147 ARG GLY ALA ILE HET FMN A 149 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 HOH *306(H2 O) HELIX 1 1 GLY A 13 GLY A 30 1 18 HELIX 2 2 ALA A 39 VAL A 41 5 3 HELIX 3 3 PHE A 71 SER A 77 1 7 HELIX 4 4 LEU A 78 THR A 81 5 4 HELIX 5 5 CYS A 102 LEU A 115 1 14 HELIX 6 6 ASP A 129 ALA A 132 5 4 HELIX 7 7 ALA A 133 GLY A 146 1 14 SHEET 1 A 5 GLU A 32 ASP A 37 0 SHEET 2 A 5 LYS A 3 GLY A 9 1 N ALA A 4 O GLU A 32 SHEET 3 A 5 LEU A 52 CYS A 57 1 O LEU A 52 N LEU A 5 SHEET 4 A 5 LYS A 87 GLY A 94 1 O LYS A 87 N VAL A 53 SHEET 5 A 5 GLU A 118 ILE A 119 1 O GLU A 118 N VAL A 88 SHEET 1 B 5 GLU A 32 ASP A 37 0 SHEET 2 B 5 LYS A 3 GLY A 9 1 N ALA A 4 O GLU A 32 SHEET 3 B 5 LEU A 52 CYS A 57 1 O LEU A 52 N LEU A 5 SHEET 4 B 5 LYS A 87 GLY A 94 1 O LYS A 87 N VAL A 53 SHEET 5 B 5 LEU A 124 ASP A 127 1 N LEU A 124 O CYS A 90 SHEET 1 C 2 THR A 59 TRP A 60 0 SHEET 2 C 2 GLU A 66 LEU A 67 -1 O GLU A 66 N TRP A 60 SITE 1 AC1 23 SER A 10 THR A 11 THR A 12 GLY A 13 SITE 2 AC1 23 ASN A 14 THR A 15 SER A 58 THR A 59 SITE 3 AC1 23 TRP A 60 GLY A 61 CYS A 93 GLY A 94 SITE 4 AC1 23 ASP A 95 TRP A 98 TYR A 100 PHE A 101 SITE 5 AC1 23 CYS A 102 HOH A 203 HOH A 205 HOH A 232 SITE 6 AC1 23 HOH A 257 HOH A 367 HOH A 487 CRYST1 41.290 55.820 32.520 90.00 100.68 90.00 P 1 21 1 2 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 0.024219 0.000000 0.004567 0.00000 SCALE2 0.000000 0.017915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031292 0.00000