HEADER ELECTRON TRANSPORT 17-JAN-07 2E83 TITLE T31V MUTANT OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS TITLE 2 (MIYAZAKI F) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FMN-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'; SOURCE 3 ORGANISM_TAXID: 883; SOURCE 4 STRAIN: MIYAZAKI F; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMKBT-100 KEYWDS BETA SHEET, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR N.SHIBATA,Y.HIGUCHI REVDAT 4 25-OCT-23 2E83 1 REMARK REVDAT 3 10-NOV-21 2E83 1 REMARK SEQADV REVDAT 2 24-FEB-09 2E83 1 VERSN REVDAT 1 15-JAN-08 2E83 0 JRNL AUTH N.SHIBATA,M.KITAMURA,Y.HIGUCHI JRNL TITL STRUCTURE OF T31V MUTANT OF FMN-BINDING PROTEIN FROM JRNL TITL 2 DESULFOVIBRIO VULGARIS MIYAZAKI F JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 699172.650 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 37117 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3716 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.52 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3082 REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE : 0.2100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 369 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1852 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 393 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 0.62000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.13 REMARK 3 ESD FROM SIGMAA (A) : 0.01 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) : 0.16 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.570 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 39.81 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : FMN.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : FMN.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2E83 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000026343. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37400 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.12200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.290 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1FLM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, SODIUM ACETATE, TRIS, PH REMARK 280 7.5, VAPOR DIFFUSION, TEMPERATURE 298K 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 42.19700 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 1123 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 2123 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FLM RELATED DB: PDB REMARK 900 RELATED ID: 1WLI RELATED DB: PDB REMARK 900 RELATED ID: 1WLK RELATED DB: PDB REMARK 900 RELATED ID: 1WLL RELATED DB: PDB DBREF 2E83 A 1 122 UNP Q46604 FMNB_DESVM 1 122 DBREF 2E83 B 1 122 UNP Q46604 FMNB_DESVM 1 122 SEQADV 2E83 VAL A 31 UNP Q46604 THR 31 ENGINEERED MUTATION SEQADV 2E83 VAL B 31 UNP Q46604 THR 31 ENGINEERED MUTATION SEQRES 1 A 122 MET LEU PRO GLY THR PHE PHE GLU VAL LEU LYS ASN GLU SEQRES 2 A 122 GLY VAL VAL ALA ILE ALA THR GLN GLY GLU ASP GLY PRO SEQRES 3 A 122 HIS LEU VAL ASN VAL TRP ASN SER TYR LEU LYS VAL LEU SEQRES 4 A 122 ASP GLY ASN ARG ILE VAL VAL PRO VAL GLY GLY MET HIS SEQRES 5 A 122 LYS THR GLU ALA ASN VAL ALA ARG ASP GLU ARG VAL LEU SEQRES 6 A 122 MET THR LEU GLY SER ARG LYS VAL ALA GLY ARG ASN GLY SEQRES 7 A 122 PRO GLY THR GLY PHE LEU ILE ARG GLY SER ALA ALA PHE SEQRES 8 A 122 ARG THR ASP GLY PRO GLU PHE GLU ALA ILE ALA ARG PHE SEQRES 9 A 122 LYS TRP ALA ARG ALA ALA LEU VAL ILE THR VAL VAL SER SEQRES 10 A 122 ALA GLU GLN THR LEU SEQRES 1 B 122 MET LEU PRO GLY THR PHE PHE GLU VAL LEU LYS ASN GLU SEQRES 2 B 122 GLY VAL VAL ALA ILE ALA THR GLN GLY GLU ASP GLY PRO SEQRES 3 B 122 HIS LEU VAL ASN VAL TRP ASN SER TYR LEU LYS VAL LEU SEQRES 4 B 122 ASP GLY ASN ARG ILE VAL VAL PRO VAL GLY GLY MET HIS SEQRES 5 B 122 LYS THR GLU ALA ASN VAL ALA ARG ASP GLU ARG VAL LEU SEQRES 6 B 122 MET THR LEU GLY SER ARG LYS VAL ALA GLY ARG ASN GLY SEQRES 7 B 122 PRO GLY THR GLY PHE LEU ILE ARG GLY SER ALA ALA PHE SEQRES 8 B 122 ARG THR ASP GLY PRO GLU PHE GLU ALA ILE ALA ARG PHE SEQRES 9 B 122 LYS TRP ALA ARG ALA ALA LEU VAL ILE THR VAL VAL SER SEQRES 10 B 122 ALA GLU GLN THR LEU HET FMN A1123 31 HET FMN B2123 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 5 HOH *393(H2 O) HELIX 1 1 PRO A 3 LYS A 11 1 9 HELIX 2 2 SER A 34 LEU A 36 5 3 HELIX 3 3 MET A 51 ASP A 61 1 11 HELIX 4 4 GLY A 95 ALA A 100 1 6 HELIX 5 5 PRO B 3 LYS B 11 1 9 HELIX 6 6 SER B 34 LEU B 36 5 3 HELIX 7 7 MET B 51 ASP B 61 1 11 HELIX 8 8 GLY B 95 ALA B 100 1 6 SHEET 1 A 7 PRO A 26 TRP A 32 0 SHEET 2 A 7 VAL A 15 GLN A 21 -1 N VAL A 16 O VAL A 31 SHEET 3 A 7 ARG A 63 ALA A 74 -1 O LEU A 65 N ALA A 19 SHEET 4 A 7 PRO A 79 ARG A 92 -1 O ILE A 85 N MET A 66 SHEET 5 A 7 ALA A 109 GLN A 120 -1 O VAL A 112 N ALA A 90 SHEET 6 A 7 ARG A 43 VAL A 48 -1 N ILE A 44 O ILE A 113 SHEET 7 A 7 LYS A 37 LEU A 39 -1 N LYS A 37 O VAL A 45 SHEET 1 B 7 GLY B 25 TRP B 32 0 SHEET 2 B 7 VAL B 15 GLY B 22 -1 N VAL B 16 O VAL B 31 SHEET 3 B 7 ARG B 63 ALA B 74 -1 O LEU B 65 N ALA B 19 SHEET 4 B 7 PRO B 79 ARG B 92 -1 O ILE B 85 N MET B 66 SHEET 5 B 7 ALA B 109 GLN B 120 -1 O VAL B 112 N ALA B 90 SHEET 6 B 7 ARG B 43 VAL B 48 -1 N ILE B 44 O ILE B 113 SHEET 7 B 7 LYS B 37 LEU B 39 -1 N LYS B 37 O VAL B 45 SITE 1 AC1 22 HIS A 27 VAL A 29 ASN A 30 VAL A 31 SITE 2 AC1 22 TRP A 32 TYR A 35 PRO A 47 VAL A 48 SITE 3 AC1 22 GLY A 49 GLY A 50 MET A 51 HIS A 52 SITE 4 AC1 22 LYS A 53 THR A 54 TRP A 106 HOH A1124 SITE 5 AC1 22 HOH A1188 HOH A1194 HOH A1260 GLY B 82 SITE 6 AC1 22 THR B 121 HOH B2126 SITE 1 AC2 23 GLY A 82 THR A 121 HOH A1126 HIS B 27 SITE 2 AC2 23 VAL B 29 ASN B 30 VAL B 31 TRP B 32 SITE 3 AC2 23 TYR B 35 PRO B 47 VAL B 48 GLY B 49 SITE 4 AC2 23 GLY B 50 MET B 51 HIS B 52 LYS B 53 SITE 5 AC2 23 THR B 54 TRP B 106 HOH B2128 HOH B2129 SITE 6 AC2 23 HOH B2165 HOH B2171 HOH B2212 CRYST1 36.615 84.394 40.387 90.00 93.33 90.00 P 1 21 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 0.027311 0.000000 0.001590 0.00000 SCALE2 0.000000 0.011849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024802 0.00000