HEADER DNA BINDING PROTEIN 19-OCT-06 2ITJ TITLE ORIGIN BINDING DOMAIN OF THE SV40 LARGE T ANTIGEN (RESIDUES 131-259). TITLE 2 P212121 CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: LARGE T ANTIGEN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ORIGIN BINDING DOMAIN (RESIDUES 131-259); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SIMIAN VIRUS 40; SOURCE 3 ORGANISM_TAXID: 10633; SOURCE 4 STRAIN: 776; SOURCE 5 GENE: LARGE T ANTIGEN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.MARTYNOWSKI,E.BOCHKAREVA,A.BOCHKAREV REVDAT 4 30-AUG-23 2ITJ 1 SEQADV REVDAT 3 24-FEB-09 2ITJ 1 VERSN REVDAT 2 13-FEB-07 2ITJ 1 JRNL REVDAT 1 12-DEC-06 2ITJ 0 JRNL AUTH E.BOCHKAREVA,D.MARTYNOWSKI,A.SEITOVA,A.BOCHKAREV JRNL TITL STRUCTURE OF THE ORIGIN-BINDING DOMAIN OF SIMIAN VIRUS 40 JRNL TITL 2 LARGE T ANTIGEN BOUND TO DNA JRNL REF EMBO J. V. 25 5961 2006 JRNL REFN ISSN 0261-4189 JRNL PMID 17139255 JRNL DOI 10.1038/SJ.EMBOJ.7601452 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.8 REMARK 3 NUMBER OF REFLECTIONS : 7693 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) : 0.215 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 821 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2010 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.557 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ITJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039996. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.5 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRIRS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8118 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43500 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2IPR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM NAAC, 20% PEG4K, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 297K 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 22.72250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.36850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.36450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.36850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.72250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.36450 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 GLY A 127 REMARK 465 SER A 128 REMARK 465 HIS A 129 REMARK 465 MET A 130 REMARK 465 LYS A 131 REMARK 465 GLY B 127 REMARK 465 SER B 128 REMARK 465 HIS B 129 REMARK 465 MET B 130 REMARK 465 LYS B 131 REMARK 465 LEU B 215 REMARK 465 CYS B 216 REMARK 465 THR B 217 REMARK 465 LYS B 253 REMARK 465 GLU B 254 REMARK 465 HIS B 255 REMARK 465 ASP B 256 REMARK 465 PHE B 257 REMARK 465 ASN B 258 REMARK 465 PRO B 259 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 ALA A 149 72.30 -108.58 REMARK 500 VAL A 181 147.50 -33.27 REMARK 500 LYS A 214 -74.33 -35.12 REMARK 500 CYS A 216 60.43 -176.78 REMARK 500 PHE A 218 19.57 49.66 REMARK 500 ASN A 258 67.22 -117.71 REMARK 500 SER B 140 -29.01 -38.66 REMARK 500 PHE B 151 115.86 -164.83 REMARK 500 VAL B 181 151.07 -46.68 REMARK 500 SER B 189 -112.76 -96.22 REMARK 500 TYR B 190 -99.75 -111.45 REMARK 500 HIS B 192 -166.53 -101.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IPR RELATED DB: PDB REMARK 900 RELATED ID: 2ITL RELATED DB: PDB REMARK 900 RELATED ID: 2NL8 RELATED DB: PDB DBREF 2ITJ A 131 259 UNP P03070 TALA_SV40 131 259 DBREF 2ITJ B 131 259 UNP P03070 TALA_SV40 131 259 SEQADV 2ITJ GLY A 127 UNP P03070 CLONING ARTIFACT SEQADV 2ITJ SER A 128 UNP P03070 CLONING ARTIFACT SEQADV 2ITJ HIS A 129 UNP P03070 CLONING ARTIFACT SEQADV 2ITJ MET A 130 UNP P03070 CLONING ARTIFACT SEQADV 2ITJ GLY B 127 UNP P03070 CLONING ARTIFACT SEQADV 2ITJ SER B 128 UNP P03070 CLONING ARTIFACT SEQADV 2ITJ HIS B 129 UNP P03070 CLONING ARTIFACT SEQADV 2ITJ MET B 130 UNP P03070 CLONING ARTIFACT SEQRES 1 A 133 GLY SER HIS MET LYS VAL GLU ASP PRO LYS ASP PHE PRO SEQRES 2 A 133 SER GLU LEU LEU SER PHE LEU SER HIS ALA VAL PHE SER SEQRES 3 A 133 ASN ARG THR LEU ALA CYS PHE ALA ILE TYR THR THR LYS SEQRES 4 A 133 GLU LYS ALA ALA LEU LEU TYR LYS LYS ILE MET GLU LYS SEQRES 5 A 133 TYR SER VAL THR PHE ILE SER ARG HIS ASN SER TYR ASN SEQRES 6 A 133 HIS ASN ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG SEQRES 7 A 133 VAL SER ALA ILE ASN ASN TYR ALA GLN LYS LEU CYS THR SEQRES 8 A 133 PHE SER PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR SEQRES 9 A 133 LEU MET TYR SER ALA LEU THR ARG ASP PRO PHE SER VAL SEQRES 10 A 133 ILE GLU GLU SER LEU PRO GLY GLY LEU LYS GLU HIS ASP SEQRES 11 A 133 PHE ASN PRO SEQRES 1 B 133 GLY SER HIS MET LYS VAL GLU ASP PRO LYS ASP PHE PRO SEQRES 2 B 133 SER GLU LEU LEU SER PHE LEU SER HIS ALA VAL PHE SER SEQRES 3 B 133 ASN ARG THR LEU ALA CYS PHE ALA ILE TYR THR THR LYS SEQRES 4 B 133 GLU LYS ALA ALA LEU LEU TYR LYS LYS ILE MET GLU LYS SEQRES 5 B 133 TYR SER VAL THR PHE ILE SER ARG HIS ASN SER TYR ASN SEQRES 6 B 133 HIS ASN ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG SEQRES 7 B 133 VAL SER ALA ILE ASN ASN TYR ALA GLN LYS LEU CYS THR SEQRES 8 B 133 PHE SER PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR SEQRES 9 B 133 LEU MET TYR SER ALA LEU THR ARG ASP PRO PHE SER VAL SEQRES 10 B 133 ILE GLU GLU SER LEU PRO GLY GLY LEU LYS GLU HIS ASP SEQRES 11 B 133 PHE ASN PRO FORMUL 3 HOH *31(H2 O) HELIX 1 1 PRO A 139 LEU A 146 5 8 HELIX 2 2 THR A 164 TYR A 179 1 16 HELIX 3 3 ARG A 204 LEU A 215 1 12 HELIX 4 4 LYS A 228 LEU A 236 1 9 HELIX 5 5 LYS A 253 PHE A 257 5 5 HELIX 6 6 LEU B 142 LEU B 146 5 5 HELIX 7 7 THR B 164 TYR B 179 1 16 HELIX 8 8 ARG B 204 LYS B 214 1 11 HELIX 9 9 LYS B 228 LEU B 236 1 9 SHEET 1 A 5 LEU A 221 GLY A 225 0 SHEET 2 A 5 LEU A 156 THR A 163 -1 N TYR A 162 O ILE A 222 SHEET 3 A 5 HIS A 192 HIS A 203 -1 O THR A 199 N ALA A 157 SHEET 4 A 5 PHE A 183 SER A 189 -1 N SER A 185 O PHE A 196 SHEET 5 A 5 SER A 242 GLU A 246 -1 O ILE A 244 N ARG A 186 SHEET 1 B 5 LEU B 221 GLY B 225 0 SHEET 2 B 5 LEU B 156 THR B 163 -1 N TYR B 162 O ILE B 222 SHEET 3 B 5 ASN B 193 HIS B 203 -1 O LEU B 195 N ILE B 161 SHEET 4 B 5 PHE B 183 ASN B 188 -1 N SER B 185 O PHE B 196 SHEET 5 B 5 SER B 242 GLU B 246 -1 O ILE B 244 N ARG B 186 CISPEP 1 ASP A 239 PRO A 240 0 -0.12 CISPEP 2 ASP B 239 PRO B 240 0 1.33 CRYST1 45.445 54.729 98.737 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 0.022005 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010128 0.00000