HEADER HYDROLASE, DNA BINDING PROTEIN 02-JUL-13 4LIF TITLE CRYSTAL STRUCTURE OF THE JCV LARGE T-ANTIGEN ORIGIN BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LARGE T ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: OBD (UNP RESIDUES 132-261); COMPND 5 SYNONYM: LT, LT-AG; COMPND 6 EC: 3.6.4.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: JC POLYOMAVIRUS; SOURCE 3 ORGANISM_COMMON: JCPYV; SOURCE 4 ORGANISM_TAXID: 10632; SOURCE 5 GENE: LARGE T ANTIGEN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PGEX-4T KEYWDS ORIGIN BINDING DOMAIN, REPLICATION, POLYOMAVIRUS, HYDROLASE, DNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.MEINKE,A.BOHM,P.BULLOCK REVDAT 3 20-SEP-23 4LIF 1 REMARK SEQADV REVDAT 2 02-APR-14 4LIF 1 JRNL REVDAT 1 05-MAR-14 4LIF 0 JRNL AUTH G.MEINKE,P.J.PHELAN,R.KALEKAR,J.SHIN,J.ARCHAMBAULT,A.BOHM, JRNL AUTH 2 P.A.BULLOCK JRNL TITL INSIGHTS INTO THE INITIATION OF JC VIRUS DNA REPLICATION JRNL TITL 2 DERIVED FROM THE CRYSTAL STRUCTURE OF THE T-ANTIGEN ORIGIN JRNL TITL 3 BINDING DOMAIN. JRNL REF PLOS PATHOG. V. 10 03966 2014 JRNL REFN ISSN 1553-7366 JRNL PMID 24586168 JRNL DOI 10.1371/JOURNAL.PPAT.1003966 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11188 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 267 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.7000 - 4.1238 1.00 2677 134 0.1408 0.1677 REMARK 3 2 4.1238 - 3.2738 1.00 2661 131 0.1866 0.2647 REMARK 3 3 3.2738 - 2.8602 1.00 2682 133 0.2444 0.3217 REMARK 3 4 2.8602 - 2.5987 0.99 2654 116 0.2815 0.3294 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.40 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1072 REMARK 3 ANGLE : 0.990 1447 REMARK 3 CHIRALITY : 0.067 154 REMARK 3 PLANARITY : 0.004 182 REMARK 3 DIHEDRAL : 14.231 380 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 133:224) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7118 -10.9615 4.7417 REMARK 3 T TENSOR REMARK 3 T11: 0.5148 T22: 0.4959 REMARK 3 T33: 0.4554 T12: 0.0647 REMARK 3 T13: 0.0204 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 6.1909 L22: 7.1521 REMARK 3 L33: 3.6224 L12: -2.1312 REMARK 3 L13: -1.3221 L23: -0.3086 REMARK 3 S TENSOR REMARK 3 S11: 0.0871 S12: -0.3937 S13: 0.0234 REMARK 3 S21: -0.2323 S22: 0.0711 S23: -0.6461 REMARK 3 S31: -0.0621 S32: -0.0498 S33: -0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 225:259) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1259 -3.0035 -6.1407 REMARK 3 T TENSOR REMARK 3 T11: 0.9113 T22: 0.7535 REMARK 3 T33: 0.8715 T12: 0.0689 REMARK 3 T13: 0.2252 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.5112 L22: 0.4112 REMARK 3 L33: 1.7185 L12: -0.3418 REMARK 3 L13: -0.0144 L23: 0.5841 REMARK 3 S TENSOR REMARK 3 S11: 0.3894 S12: 1.0828 S13: 0.7163 REMARK 3 S21: -0.6562 S22: 0.1446 S23: -0.7360 REMARK 3 S31: -0.9557 S32: 0.4574 S33: 0.0033 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4LIF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5906 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 14.70 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.6000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2FUF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 0.2 M LISO4, 30 % PEG REMARK 280 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 273K, PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 51.89650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 51.89650 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.43000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.89650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.71500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.89650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.14500 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.89650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.89650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 17.43000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 51.89650 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 26.14500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 51.89650 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 8.71500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 130 REMARK 465 SER A 131 REMARK 465 LYS A 132 REMARK 465 PRO A 260 REMARK 465 GLU A 261 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 LYS A 229 CG CD CE NZ 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 218 -57.36 -123.93 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 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NBP RELATED DB: PDB REMARK 900 RELATED ID: 4LMD RELATED DB: PDB DBREF 4LIF A 132 261 UNP P03072 LT_POVJC 132 261 SEQADV 4LIF GLY A 130 UNP P03072 EXPRESSION TAG SEQADV 4LIF SER A 131 UNP P03072 EXPRESSION TAG SEQRES 1 A 132 GLY SER LYS VAL GLU ASP PRO LYS ASP PHE PRO VAL ASP SEQRES 2 A 132 LEU HIS ALA PHE LEU SER GLN ALA VAL PHE SER ASN ARG SEQRES 3 A 132 THR VAL ALA SER PHE ALA VAL TYR THR THR LYS GLU LYS SEQRES 4 A 132 ALA GLN ILE LEU TYR LYS LYS LEU MET GLU LYS TYR SER SEQRES 5 A 132 VAL THR PHE ILE SER ARG HIS GLY PHE GLY GLY HIS ASN SEQRES 6 A 132 ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG VAL SER SEQRES 7 A 132 ALA ILE ASN ASN TYR CYS GLN LYS LEU CYS THR PHE SER SEQRES 8 A 132 PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR LEU PHE SEQRES 9 A 132 TYR SER ALA LEU CYS ARG GLN PRO TYR ALA VAL VAL GLU SEQRES 10 A 132 GLU SER ILE GLN GLY GLY LEU LYS GLU HIS ASP PHE ASN SEQRES 11 A 132 PRO GLU HET SO4 A 301 5 HET SO4 A 302 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *5(H2 O) HELIX 1 1 PRO A 140 ALA A 145 5 6 HELIX 2 2 LYS A 166 TYR A 180 1 15 HELIX 3 3 ARG A 205 LYS A 215 1 11 HELIX 4 4 LYS A 229 LEU A 237 1 9 HELIX 5 5 LYS A 254 PHE A 258 5 5 SHEET 1 A 6 LEU A 147 SER A 148 0 SHEET 2 A 6 ILE A 223 VAL A 227 -1 O GLY A 226 N SER A 148 SHEET 3 A 6 VAL A 157 THR A 165 -1 N TYR A 163 O ILE A 223 SHEET 4 A 6 HIS A 193 HIS A 204 -1 O HIS A 204 N VAL A 157 SHEET 5 A 6 PHE A 184 PHE A 190 -1 N SER A 186 O PHE A 197 SHEET 6 A 6 ALA A 243 GLU A 247 -1 O ALA A 243 N GLY A 189 CISPEP 1 GLN A 240 PRO A 241 0 3.62 SITE 1 AC1 5 LYS A 168 CYS A 217 THR A 218 PHE A 219 SITE 2 AC1 5 SER A 220 SITE 1 AC2 4 HIS A 202 ARG A 203 ARG A 205 HOH A 401 CRYST1 103.793 103.793 34.860 90.00 90.00 90.00 I 41 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 0.009635 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028686 0.00000