PDB Short entry for 1D8L HEADER GENE REGULATION 25-OCT-99 1D8L TITLE E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING TITLE 2 DOMAIN III COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: NH2 REGION; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS OB-FOLD, HELIX-HAIRPIN-HELIX MOTIF, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR T.NISHINO,H.IWASAKI,M.KATAOKA,M.ARIYOSHI,T.FUJITA,H.SHINAGAWA, AUTHOR 2 K.MORIKAWA REVDAT 4 07-FEB-24 1D8L 1 REMARK REVDAT 3 04-APR-18 1D8L 1 REMARK REVDAT 2 24-FEB-09 1D8L 1 VERSN REVDAT 1 03-MAY-00 1D8L 0 JRNL AUTH T.NISHINO,H.IWASAKI,M.KATAOKA,M.ARIYOSHI,T.FUJITA, JRNL AUTH 2 H.SHINAGAWA,K.MORIKAWA JRNL TITL MODULATION OF RUVB FUNCTION BY THE MOBILE DOMAIN III OF THE JRNL TITL 2 HOLLIDAY JUNCTION RECOGNITION PROTEIN RUVA. JRNL REF J.MOL.BIOL. V. 298 407 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10772859 JRNL DOI 10.1006/JMBI.2000.3675 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 9523 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.320 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 471 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2192 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009889. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.60 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 : OTHER 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2020 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10073 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.3000 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 39.80000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.80000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.80000 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: TETRAMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 115.60000 REMARK 350 BIOMT3 2 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 THR A 141 REMARK 465 PRO A 142 REMARK 465 ALA A 143 REMARK 465 ALA A 144 REMARK 465 ASP A 145 REMARK 465 LEU A 146 REMARK 465 VAL A 147 REMARK 465 LEU A 148 REMARK 465 THR A 149 REMARK 465 THR B 141 REMARK 465 PRO B 142 REMARK 465 ALA B 143 REMARK 465 ALA B 144 REMARK 465 ASP B 145 REMARK 465 LEU B 146 REMARK 465 VAL B 147 REMARK 465 LEU B 148 REMARK 465 THR B 149 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 PRO A 14 128.62 -39.41 REMARK 500 PRO A 39 156.92 -49.25 REMARK 500 ILE A 116 -77.42 -77.90 REMARK 500 PRO B 14 126.17 -37.70 REMARK 500 PRO B 39 -173.84 -62.51 REMARK 500 GLU B 105 33.68 77.03 REMARK 500 ILE B 116 -73.58 -85.44 REMARK 500 LEU B 135 -171.73 -171.71 REMARK 500 REMARK 500 REMARK: NULL DBREF 1D8L A 1 149 UNP P0A809 RUVA_ECOLI 1 149 DBREF 1D8L B 1 149 UNP P0A809 RUVA_ECOLI 1 149 SEQRES 1 A 149 MET ILE GLY ARG LEU ARG GLY ILE ILE ILE GLU LYS GLN SEQRES 2 A 149 PRO PRO LEU VAL LEU ILE GLU VAL GLY GLY VAL GLY TYR SEQRES 3 A 149 GLU VAL HIS MET PRO MET THR CYS PHE TYR GLU LEU PRO SEQRES 4 A 149 GLU ALA GLY GLN GLU ALA ILE VAL PHE THR HIS PHE VAL SEQRES 5 A 149 VAL ARG GLU ASP ALA GLN LEU LEU TYR GLY PHE ASN ASN SEQRES 6 A 149 LYS GLN GLU ARG THR LEU PHE LYS GLU LEU ILE LYS THR SEQRES 7 A 149 ASN GLY VAL GLY PRO LYS LEU ALA LEU ALA ILE LEU SER SEQRES 8 A 149 GLY MET SER ALA GLN GLN PHE VAL ASN ALA VAL GLU ARG SEQRES 9 A 149 GLU GLU VAL GLY ALA LEU VAL LYS LEU PRO GLY ILE GLY SEQRES 10 A 149 LYS LYS THR ALA GLU ARG LEU ILE VAL GLU MET LYS ASP SEQRES 11 A 149 ARG PHE LYS GLY LEU HIS GLY ASP LEU PHE THR PRO ALA SEQRES 12 A 149 ALA ASP LEU VAL LEU THR SEQRES 1 B 149 MET ILE GLY ARG LEU ARG GLY ILE ILE ILE GLU LYS GLN SEQRES 2 B 149 PRO PRO LEU VAL LEU ILE GLU VAL GLY GLY VAL GLY TYR SEQRES 3 B 149 GLU VAL HIS MET PRO MET THR CYS PHE TYR GLU LEU PRO SEQRES 4 B 149 GLU ALA GLY GLN GLU ALA ILE VAL PHE THR HIS PHE VAL SEQRES 5 B 149 VAL ARG GLU ASP ALA GLN LEU LEU TYR GLY PHE ASN ASN SEQRES 6 B 149 LYS GLN GLU ARG THR LEU PHE LYS GLU LEU ILE LYS THR SEQRES 7 B 149 ASN GLY VAL GLY PRO LYS LEU ALA LEU ALA ILE LEU SER SEQRES 8 B 149 GLY MET SER ALA GLN GLN PHE VAL ASN ALA VAL GLU ARG SEQRES 9 B 149 GLU GLU VAL GLY ALA LEU VAL LYS LEU PRO GLY ILE GLY SEQRES 10 B 149 LYS LYS THR ALA GLU ARG LEU ILE VAL GLU MET LYS ASP SEQRES 11 B 149 ARG PHE LYS GLY LEU HIS GLY ASP LEU PHE THR PRO ALA SEQRES 12 B 149 ALA ASP LEU VAL LEU THR FORMUL 3 HOH *22(H2 O) HELIX 1 1 PRO A 31 GLU A 37 5 7 HELIX 2 2 ASN A 65 ILE A 76 1 12 HELIX 3 3 GLY A 82 MET A 93 1 12 HELIX 4 4 SER A 94 ARG A 104 1 11 HELIX 5 5 GLU A 106 LEU A 113 1 8 HELIX 6 6 GLY A 117 LYS A 133 1 17 HELIX 7 7 PRO B 31 LEU B 38 1 8 HELIX 8 8 ASN B 65 ILE B 76 1 12 HELIX 9 9 GLY B 82 GLY B 92 1 11 HELIX 10 10 SER B 94 GLU B 105 1 12 HELIX 11 11 GLU B 106 LYS B 112 1 7 HELIX 12 12 GLY B 117 LYS B 133 1 17 SHEET 1 A 6 ARG A 4 GLN A 13 0 SHEET 2 A 6 LEU A 16 VAL A 21 -1 N LEU A 16 O GLN A 13 SHEET 3 A 6 VAL A 24 HIS A 29 -1 O VAL A 24 N VAL A 21 SHEET 4 A 6 ALA A 57 PHE A 63 1 O LEU A 60 N HIS A 29 SHEET 5 A 6 GLU A 44 ARG A 54 -1 O PHE A 48 N PHE A 63 SHEET 6 A 6 ARG A 4 GLN A 13 -1 O LEU A 5 N VAL A 47 SHEET 1 B 6 ARG B 4 GLN B 13 0 SHEET 2 B 6 LEU B 16 VAL B 21 -1 N LEU B 16 O GLN B 13 SHEET 3 B 6 VAL B 24 HIS B 29 -1 O VAL B 24 N VAL B 21 SHEET 4 B 6 ALA B 57 PHE B 63 1 O LEU B 60 N HIS B 29 SHEET 5 B 6 GLU B 44 ARG B 54 -1 N PHE B 48 O PHE B 63 SHEET 6 B 6 ARG B 4 GLN B 13 -1 O LEU B 5 N VAL B 47 CISPEP 1 PRO A 14 PRO A 15 0 6.98 CISPEP 2 PRO B 14 PRO B 15 0 6.68 CRYST1 79.600 115.600 34.800 90.00 90.00 90.00 P 21 21 2 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 0.012555 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028711 0.00000