HEADER ELECTRON TRANSPORT 27-APR-09 3A20 TITLE L122K 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 KEYWDS BETA SHEET, CYTOPLASM, ELECTRON TRANSPORT, FLAVOPROTEIN, FMN, KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR N.SHIBATA,Y.HIGUCHI REVDAT 3 01-NOV-23 3A20 1 REMARK REVDAT 2 10-NOV-21 3A20 1 REMARK SEQADV REVDAT 1 19-MAY-09 3A20 0 SPRSDE 19-MAY-09 3A20 1WLL JRNL AUTH M.KITAMURA,K.TERAKAWA,H.INOUE,T.HAYASHIDA,K.SUTO,Y.MORIMOTO, JRNL AUTH 2 N.YASUOKA,N.SHIBATA,Y.HIGUCHI JRNL TITL DETERMINATION OF THE ROLE OF THE CARBOXYL-TERMINAL JRNL TITL 2 LEUCINE-122 IN FMN-BINDING PROTEIN BY MUTATIONAL AND JRNL TITL 3 STRUCTURAL ANALYSIS JRNL REF J.BIOCHEM. V. 141 459 2007 JRNL REFN ISSN 0021-924X JRNL PMID 17261542 JRNL DOI 10.1093/JB/MVM051 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 339289.050 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 29879 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) : 0.170 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1473 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1981 REMARK 3 BIN R VALUE (WORKING SET) : 0.1650 REMARK 3 BIN FREE R VALUE : 0.1870 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 99 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1854 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 276 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64000 REMARK 3 B22 (A**2) : 0.99000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.00 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) : 0.06 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 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) : 1.070 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.660 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.850 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 47.19 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 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3A20 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000028711. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-02 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 : BL40B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30132 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.08900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 16.70 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 (%): 47.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, SODIUM ACETATE, TRIS, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, 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 41.65950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 123 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 123 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WLK RELATED DB: PDB REMARK 900 L122E MUTANT REMARK 900 RELATED ID: 1WKI RELATED DB: PDB REMARK 900 L122Y MUTANT REMARK 900 RELATED ID: 1FLM RELATED DB: PDB REMARK 900 WILD TYPE DBREF 3A20 A 1 122 UNP Q46604 FMNB_DESVM 1 122 DBREF 3A20 B 1 122 UNP Q46604 FMNB_DESVM 1 122 SEQADV 3A20 LYS A 122 UNP Q46604 LEU 122 ENGINEERED MUTATION SEQADV 3A20 LYS B 122 UNP Q46604 LEU 122 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 THR 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 LYS 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 THR 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 LYS HET FMN A 123 31 HET FMN B 123 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 5 HOH *276(H2 O) HELIX 1 1 PRO A 3 LEU A 10 1 8 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 LEU B 10 1 8 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 GLY A 25 TRP A 32 0 SHEET 2 A 7 VAL A 15 GLY A 22 -1 N ILE A 18 O VAL A 29 SHEET 3 A 7 ARG A 63 SER A 70 -1 O LEU A 65 N ALA A 19 SHEET 4 A 7 THR A 81 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 LEU A 39 O ARG A 43 SHEET 1 B 7 GLY B 25 TRP B 32 0 SHEET 2 B 7 VAL B 15 GLY B 22 -1 N ILE B 18 O VAL B 29 SHEET 3 B 7 ARG B 63 SER B 70 -1 O LEU B 65 N ALA B 19 SHEET 4 B 7 THR B 81 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 21 HIS A 27 VAL A 29 ASN A 30 THR A 31 SITE 2 AC1 21 TRP A 32 TYR A 35 PRO A 47 VAL A 48 SITE 3 AC1 21 GLY A 49 GLY A 50 MET A 51 HIS A 52 SITE 4 AC1 21 LYS A 53 THR A 54 TRP A 106 HOH A 139 SITE 5 AC1 21 HOH A 187 HOH A 215 GLY B 82 THR B 121 SITE 6 AC1 21 HOH B 177 SITE 1 AC2 22 GLY A 82 THR A 121 HOH A 133 HIS B 27 SITE 2 AC2 22 VAL B 29 ASN B 30 THR B 31 TRP B 32 SITE 3 AC2 22 TYR B 35 PRO B 47 GLY B 49 GLY B 50 SITE 4 AC2 22 MET B 51 HIS B 52 LYS B 53 THR B 54 SITE 5 AC2 22 TRP B 106 HOH B 185 HOH B 211 HOH B 223 SITE 6 AC2 22 HOH B 233 HOH B 248 CRYST1 36.724 83.319 40.408 90.00 93.86 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 0.027230 0.000000 0.001835 0.00000 SCALE2 0.000000 0.012002 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024804 0.00000