HEADER ELECTRON TRANSPORT 10-MAR-99 1FLM TITLE DIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (FMN-BINDING PROTEIN); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: 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 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 9 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMKBT-100 KEYWDS FMN BINDING, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR K.SUTO,K.KAWAGOE,N.SHIBATA,K.MORIMOTO,Y.HIGUCHI,M.KITAMURA,T.NAKAYA, AUTHOR 2 N.YASUOKA REVDAT 4 27-DEC-23 1FLM 1 REMARK REVDAT 3 26-NOV-14 1FLM 1 REMARK VERSN REVDAT 2 24-FEB-09 1FLM 1 VERSN REVDAT 1 06-MAR-00 1FLM 0 JRNL AUTH K.SUTO,K.KAWAGOE,N.SHIBATA,Y.MORIMOTO,Y.HIGUCHI,M.KITAMURA, JRNL AUTH 2 T.NAKAYA,N.YASUOKA JRNL TITL HOW DO THE X-RAY STRUCTURE AND THE NMR STRUCTURE OF JRNL TITL 2 FMN-BINDING PROTEIN DIFFER? JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 368 2000 JRNL REFN ISSN 0907-4449 JRNL PMID 10713530 JRNL DOI 10.1107/S0907444900000111 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)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.6 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.150 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5694 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 51465 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)) : 0.144 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 4974 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 44768 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 : 200 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) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.030 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 : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FLM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B 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 : SI(111) REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68514 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.16300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG6000, 0.1M TRIS(PH7.5), 20% REMARK 280 GRYCEROL, 0.2M NACL 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 42.30000 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: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10660 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 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 ARG A 92 CD - NE - CZ ANGL. DEV. = 19.1 DEGREES REMARK 500 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 43 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 PHE B 83 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES 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 123 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 123 DBREF 1FLM A 1 122 UNP Q46604 FMNB_DESVM 1 122 DBREF 1FLM B 1 122 UNP Q46604 FMNB_DESVM 1 122 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 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 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 LEU 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 *200(H2 O) HELIX 1 H1 GLY A 4 LEU A 10 1 7 HELIX 2 H2 SER A 34 TYR A 35 5 2 HELIX 3 H3 HIS A 52 ARG A 60 1 9 HELIX 4 H4 PRO A 96 GLU A 99 1 4 HELIX 5 H5 GLY B 4 LEU B 10 1 7 HELIX 6 H6 SER B 34 TYR B 35 5 2 SHEET 1 S1 7 PRO A 26 TRP A 32 0 SHEET 2 S1 7 VAL A 15 GLN A 21 0 SHEET 3 S1 7 ARG A 63 ALA A 74 0 SHEET 4 S1 7 PRO A 79 ARG A 92 0 SHEET 5 S1 7 ALA A 109 GLN A 120 0 SHEET 6 S1 7 ARG A 43 VAL A 48 0 SHEET 7 S1 7 LYS A 37 LEU A 39 0 SHEET 1 S2 7 PRO B 26 TRP B 32 0 SHEET 2 S2 7 VAL B 15 GLN B 21 0 SHEET 3 S2 7 ARG B 63 ALA B 74 0 SHEET 4 S2 7 PRO B 79 ARG B 92 0 SHEET 5 S2 7 ALA B 109 GLN B 120 0 SHEET 6 S2 7 ARG B 43 VAL B 48 0 SHEET 7 S2 7 LYS B 37 LEU B 39 0 SITE 1 AC1 19 HIS A 27 VAL A 29 ASN A 30 THR A 31 SITE 2 AC1 19 TRP A 32 TYR A 35 PRO A 47 GLY A 49 SITE 3 AC1 19 GLY A 50 MET A 51 HIS A 52 LYS A 53 SITE 4 AC1 19 THR A 54 HOH A1025 HOH A1026 HOH A1028 SITE 5 AC1 19 HOH A1084 GLY B 82 THR B 121 SITE 1 AC2 21 GLY A 82 THR A 121 HOH A1022 HOH A1148 SITE 2 AC2 21 HIS B 27 VAL B 29 ASN B 30 THR B 31 SITE 3 AC2 21 TRP B 32 TYR B 35 PRO B 47 GLY B 49 SITE 4 AC2 21 GLY B 50 MET B 51 HIS B 52 LYS B 53 SITE 5 AC2 21 THR B 54 HOH B1053 HOH B1083 HOH B1107 SITE 6 AC2 21 HOH B1196 CRYST1 37.230 84.600 41.110 90.00 94.10 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 0.026860 0.000000 0.001925 0.00000 SCALE2 0.000000 0.011820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024387 0.00000 MTRIX1 1 -0.999990 0.004270 0.002020 57.06046 1 MTRIX2 1 -0.003350 -0.340220 -0.940340 41.57248 1 MTRIX3 1 -0.003330 -0.940340 0.340230 29.22138 1