HEADER UNKNOWN FUNCTION 18-APR-03 1UCR TITLE THREE-DIMENSIONAL CRYSTAL STRUCTURE OF DISSIMILATORY SULFITE REDUCTASE TITLE 2 D (DSRD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DSVD; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DISSIMILATORY SULFITE REDUCTASE D, DSRD; COMPND 5 ENGINEERED: 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 DISSIMILATORY SULFITE REDUCTASE D, DNA BINDING MOTIF, SULFATE- KEYWDS 2 REDUCING BACTERIA, WINGED-HELIX MOTIF, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR N.MIZUNO,G.VOORDOUW,K.MIKI,A.SARAI,Y.HIGUCHI REVDAT 3 27-DEC-23 1UCR 1 REMARK REVDAT 2 24-FEB-09 1UCR 1 VERSN REVDAT 1 14-OCT-03 1UCR 0 JRNL AUTH N.MIZUNO,G.VOORDOUW,K.MIKI,A.SARAI,Y.HIGUCHI JRNL TITL CRYSTAL STRUCTURE OF DISSIMILATORY SULFITE REDUCTASE D JRNL TITL 2 (DSRD) PROTEIN-POSSIBLE INTERACTION WITH B- AND Z-DNA BY ITS JRNL TITL 3 WINGED-HELIX MOTIF JRNL REF STRUCTURE V. 11 1133 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12962631 JRNL DOI 10.1016/S0969-2126(03)00156-4 REMARK 2 REMARK 2 RESOLUTION. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 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) : 0.139 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.138 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5629 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 55430 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.136 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)) : 45797 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1176 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1451.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 6 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 13068 REMARK 3 NUMBER OF RESTRAINTS : 15368 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.035 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.071 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.100 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.060 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.073 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.106 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UCR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000005683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.708 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55639 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: SIRAS 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 (%): 45.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 73-75% SATURATED AMMONIUM SULFATE, PH REMARK 280 5.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 30.01250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.60900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.27950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.60900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.01250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.27950 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 75 REMARK 465 HIS A 76 REMARK 465 GLU A 77 REMARK 465 ASP A 78 REMARK 465 HIS B 76 REMARK 465 GLU B 77 REMARK 465 ASP B 78 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 SER A 16 OG 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 SER A 16 CA - C - N ANGL. DEV. = 19.3 DEGREES REMARK 500 SER A 16 O - C - N ANGL. DEV. = -13.8 DEGREES REMARK 500 GLY A 17 C - N - CA ANGL. DEV. = -19.3 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 GLN A 71 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 GLN A 71 CG - CD - NE2 ANGL. DEV. = 15.1 DEGREES REMARK 500 ASP B 33 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 GLN B 36 N - CA - CB ANGL. DEV. = -11.0 DEGREES REMARK 500 GLN B 36 CG - CD - NE2 ANGL. DEV. = 18.2 DEGREES REMARK 500 ARG B 37 NH1 - CZ - NH2 ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG B 37 NE - CZ - NH1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 37 NE - CZ - NH2 ANGL. DEV. = -3.5 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 THR A 60 -148.96 -143.65 REMARK 500 THR B 60 -156.38 -134.50 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 SO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 205 DBREF 1UCR A 1 78 UNP Q46582 DSVD_DESVH 1 78 DBREF 1UCR B 1 78 UNP Q46582 DSVD_DESVH 1 78 SEQRES 1 A 78 MET GLU GLU ALA LYS GLN LYS VAL VAL ASP PHE LEU ASN SEQRES 2 A 78 SER LYS SER GLY SER LYS SER LYS PHE TYR PHE ASN ASP SEQRES 3 A 78 PHE THR ASP LEU PHE PRO ASP MET LYS GLN ARG GLU VAL SEQRES 4 A 78 LYS LYS ILE LEU THR ALA LEU VAL ASN ASP GLU VAL LEU SEQRES 5 A 78 GLU TYR TRP SER SER GLY SER THR THR MET TYR GLY LEU SEQRES 6 A 78 LYS GLY ALA GLY LYS GLN ALA ALA ALA GLU HIS GLU ASP SEQRES 1 B 78 MET GLU GLU ALA LYS GLN LYS VAL VAL ASP PHE LEU ASN SEQRES 2 B 78 SER LYS SER GLY SER LYS SER LYS PHE TYR PHE ASN ASP SEQRES 3 B 78 PHE THR ASP LEU PHE PRO ASP MET LYS GLN ARG GLU VAL SEQRES 4 B 78 LYS LYS ILE LEU THR ALA LEU VAL ASN ASP GLU VAL LEU SEQRES 5 B 78 GLU TYR TRP SER SER GLY SER THR THR MET TYR GLY LEU SEQRES 6 B 78 LYS GLY ALA GLY LYS GLN ALA ALA ALA GLU HIS GLU ASP HET SO4 A 202 5 HET SO4 A 205 5 HET SO4 B 201 5 HET SO4 B 203 5 HET SO4 B 204 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *231(H2 O) HELIX 1 1 GLU A 2 ASN A 13 1 12 HELIX 2 2 SER A 14 LYS A 19 1 6 HELIX 3 3 PHE A 24 PHE A 31 1 8 HELIX 4 4 LYS A 35 ASP A 49 1 15 HELIX 5 5 GLY A 67 ALA A 74 1 8 HELIX 6 6 GLU B 2 ASN B 13 1 12 HELIX 7 7 PHE B 24 PHE B 31 1 8 HELIX 8 8 LYS B 35 ASP B 49 1 15 HELIX 9 9 GLY B 67 GLU B 75 1 9 SHEET 1 A 3 PHE A 22 TYR A 23 0 SHEET 2 A 3 THR A 60 LEU A 65 -1 O TYR A 63 N PHE A 22 SHEET 3 A 3 LEU A 52 SER A 57 -1 N GLU A 53 O GLY A 64 SHEET 1 B 3 PHE B 22 TYR B 23 0 SHEET 2 B 3 THR B 60 LEU B 65 -1 O TYR B 63 N PHE B 22 SHEET 3 B 3 LEU B 52 SER B 57 -1 N SER B 57 O THR B 60 SITE 1 AC1 6 HOH A 335 HOH A 389 LYS B 35 GLN B 36 SITE 2 AC1 6 ARG B 37 HOH B 418 SITE 1 AC2 5 MET A 1 GLU A 2 LYS A 5 HOH A 383 SITE 2 AC2 5 HOH A 422 SITE 1 AC3 3 MET B 1 GLU B 2 LYS B 5 SITE 1 AC4 7 SER A 56 TYR B 23 PHE B 24 ASN B 25 SITE 2 AC4 7 THR B 60 THR B 61 HOH B 456 SITE 1 AC5 11 TYR A 23 PHE A 24 ASN A 25 ASP A 26 SITE 2 AC5 11 THR A 60 THR A 61 HOH A 322 HOH A 331 SITE 3 AC5 11 HOH A 375 ASP B 29 SER B 56 CRYST1 60.025 64.559 45.218 90.00 90.00 90.00 P 21 21 21 8 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 0.016660 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015490 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022115 0.00000