HEADER RECOMBINATION 04-FEB-12 4DKS TITLE A SPINDLE-SHAPED VIRUS PROTEIN (CHYMOTRYPSIN TREATED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE INTEGRASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS VIRUS 1; SOURCE 3 ORGANISM_TAXID: 244589; SOURCE 4 GENE: D335; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30A(+) KEYWDS CATALYTIC DOMAIN, INTEGRASE, THE C174 DOMAIN OF SSV1 INT, SEVEN- KEYWDS 2 HELICES, THREE-STRANDED ANTIPARALLEL-SHEET', RECOMBINATION EXPDTA X-RAY DIFFRACTION AUTHOR S.OUYANG,W.LIANG,L.HUANG,Z.-J.LIU REVDAT 2 01-JAN-20 4DKS 1 JRNL REVDAT 1 30-MAY-12 4DKS 0 JRNL AUTH Z.ZHAN,S.OUYANG,W.LIANG,Z.ZHANG,Z.J.LIU,L.HUANG JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THE C-TERMINAL JRNL TITL 2 CATALYTIC DOMAIN OF SSV1 INTEGRASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 659 2012 JRNL REFN ESSN 1399-0047 JRNL PMID 22683788 JRNL DOI 10.1107/S0907444912007202 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8010 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 378 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 40.4958 - 3.8934 1.00 2671 117 0.2059 0.2486 REMARK 3 2 3.8934 - 3.0906 1.00 2502 132 0.1836 0.2739 REMARK 3 3 3.0906 - 2.7000 1.00 2459 129 0.2289 0.2763 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 38.02 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.08390 REMARK 3 B22 (A**2) : -1.08390 REMARK 3 B33 (A**2) : 2.16780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 1226 REMARK 3 ANGLE : 1.072 1648 REMARK 3 CHIRALITY : 0.073 181 REMARK 3 PLANARITY : 0.006 202 REMARK 3 DIHEDRAL : 15.769 459 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4DKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070453. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8010 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL OR MGCL2, 0.1M HEPES, REMARK 280 25%(W/V) POLYETHYLENE GLYCOL 3350, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 48.04550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.61200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.61200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.02275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.61200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.61200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.06825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.61200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.61200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.02275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.61200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.61200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 72.06825 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.04550 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 TRP A 238 REMARK 465 THR A 239 REMARK 465 ARG A 240 REMARK 465 GLY A 241 REMARK 465 TYR A 242 REMARK 465 LYS A 243 REMARK 465 LYS A 272 REMARK 465 ASP A 273 REMARK 465 THR A 307 REMARK 465 ARG A 308 REMARK 465 VAL A 309 REMARK 465 LEU A 310 REMARK 465 THR A 311 REMARK 465 GLN A 312 REMARK 465 HIS A 313 REMARK 465 TYR A 314 REMARK 465 VAL A 335 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 THR A 187 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N ALA A 274 O HOH A 433 2.17 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 ASP A 175 116.46 -167.84 REMARK 500 GLU A 221 51.69 -141.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VCF RELATED DB: PDB REMARK 900 RE-CLONED REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FULL SEQUENCE WHICH WAS PREPARED REMARK 999 FOR THE CRYSTLLIZATION IS AS FOLLOWS. REMARK 999 REMARK 999 MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGS REMARK 999 MTKDKTRYKYGDYILRERKGRYYVYKLEYENGEVKERYVGPLADVVESYL REMARK 999 KMKLGVVGDTPLQADPPGFEPGTSGSGGGKEGTERRKIALVANLRQYATD REMARK 999 GNIKAFYDYLMNERGISEKTAKDYINAISKPYKETRDAQKAYRLFARFLA REMARK 999 SRNIIHDEFADKILKAVKVKKANADIYIPTLEEIKRTLQLAKDYSENVYF REMARK 999 IYRIALESGVRLSEILKVLKEPERDICGNDVCYYPLSWTRGYKGVFYVFH REMARK 999 ITPLKRVEVTKWAIADFERRHKDAIAIKYFRKFVASKMAELSVPLDIIDF REMARK 999 IQGRKPTRVLTQHYVSLFGIAKEQYKKYAEWLKGV REMARK 999 REMARK 999 HOWEVER, THE PROTEIN WAS CRYSTALLIZED BY IN REMARK 999 SITU PROTEOLYSIS METHODS (CHYMOTRYPSIN TREATED). REMARK 999 THE N-TERMINAL AND SOME LOOPS MISSED IN THE STRUCTURE. DBREF 4DKS A 174 335 UNP P20214 INTG_SSV1 174 335 SEQRES 1 A 162 ALA ASP ILE TYR ILE PRO THR LEU GLU GLU ILE LYS ARG SEQRES 2 A 162 THR LEU GLN LEU ALA LYS ASP TYR SER GLU ASN VAL TYR SEQRES 3 A 162 PHE ILE TYR ARG ILE ALA LEU GLU SER GLY VAL ARG LEU SEQRES 4 A 162 SER GLU ILE LEU LYS VAL LEU LYS GLU PRO GLU ARG ASP SEQRES 5 A 162 ILE CYS GLY ASN ASP VAL CYS TYR TYR PRO LEU SER TRP SEQRES 6 A 162 THR ARG GLY TYR LYS GLY VAL PHE TYR VAL PHE HIS ILE SEQRES 7 A 162 THR PRO LEU LYS ARG VAL GLU VAL THR LYS TRP ALA ILE SEQRES 8 A 162 ALA ASP PHE GLU ARG ARG HIS LYS ASP ALA ILE ALA ILE SEQRES 9 A 162 LYS TYR PHE ARG LYS PHE VAL ALA SER LYS MET ALA GLU SEQRES 10 A 162 LEU SER VAL PRO LEU ASP ILE ILE ASP PHE ILE GLN GLY SEQRES 11 A 162 ARG LYS PRO THR ARG VAL LEU THR GLN HIS TYR VAL SER SEQRES 12 A 162 LEU PHE GLY ILE ALA LYS GLU GLN TYR LYS LYS TYR ALA SEQRES 13 A 162 GLU TRP LEU LYS GLY VAL FORMUL 2 HOH *67(H2 O) HELIX 1 1 THR A 180 SER A 195 1 16 HELIX 2 2 SER A 195 GLY A 209 1 15 HELIX 3 3 ARG A 211 LEU A 219 1 9 HELIX 4 4 GLU A 221 ASP A 225 5 5 HELIX 5 5 THR A 260 ARG A 270 1 11 HELIX 6 6 ALA A 276 LYS A 278 5 3 HELIX 7 7 TYR A 279 LEU A 291 1 13 HELIX 8 8 PRO A 294 GLN A 302 1 9 HELIX 9 9 SER A 316 GLY A 334 1 19 SHEET 1 A 3 ILE A 226 CYS A 227 0 SHEET 2 A 3 CYS A 232 PRO A 235 -1 O TYR A 233 N ILE A 226 SHEET 3 A 3 TYR A 247 HIS A 250 -1 O HIS A 250 N CYS A 232 SSBOND 1 CYS A 227 CYS A 232 1555 1555 2.07 CRYST1 75.224 75.224 96.091 90.00 90.00 90.00 P 41 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 0.013294 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013294 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010407 0.00000