HEADER TRANSCRIPTION 30-SEP-10 3P1G TITLE CRYSTAL STRUCTURE OF THE XENOTROPIC MURINE LEUKEMIA VIRUS-RELATED TITLE 2 VIRUS (XMRV) RNASE H DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: XENOTROPIC MURINE LEUKEMIA VIRUS-RELATED VIRUS (XMRV) RNASE COMPND 3 H DOMAIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOTROPIC MULV-RELATED VIRUS; SOURCE 3 ORGANISM_TAXID: 438045; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS XMRV, RNASE H, REVERSE TRANSCRIPTASE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.A.KIRBY,S.G.SARAFIANOS REVDAT 4 21-FEB-24 3P1G 1 REMARK SEQADV LINK REVDAT 3 04-APR-12 3P1G 1 JRNL REVDAT 2 01-FEB-12 3P1G 1 JRNL VERSN REVDAT 1 13-OCT-10 3P1G 0 JRNL AUTH K.A.KIRBY,B.MARCHAND,Y.T.ONG,T.P.NDONGWE,A.HACHIYA, JRNL AUTH 2 E.MICHAILIDIS,M.D.LESLIE,D.V.SIETSEMA,T.L.FETTERLY, JRNL AUTH 3 C.A.DORST,K.SINGH,Z.WANG,M.A.PARNIAK,S.G.SARAFIANOS JRNL TITL STRUCTURAL AND INHIBITION STUDIES OF THE RNASE H FUNCTION OF JRNL TITL 2 XENOTROPIC MURINE LEUKEMIA VIRUS-RELATED VIRUS REVERSE JRNL TITL 3 TRANSCRIPTASE. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 56 2048 2012 JRNL REFN ISSN 0066-4804 JRNL PMID 22252812 JRNL DOI 10.1128/AAC.06000-11 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 21970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1122 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 37.5417 - 2.9998 1.00 2663 142 0.1526 0.1531 REMARK 3 2 2.9998 - 2.3811 1.00 2637 134 0.1584 0.1907 REMARK 3 3 2.3811 - 2.0802 1.00 2612 156 0.1551 0.1807 REMARK 3 4 2.0802 - 1.8900 0.99 2648 124 0.1569 0.1943 REMARK 3 5 1.8900 - 1.7545 0.99 2593 148 0.1853 0.2302 REMARK 3 6 1.7545 - 1.6511 0.99 2587 126 0.2048 0.2932 REMARK 3 7 1.6511 - 1.5684 0.99 2611 145 0.1783 0.2128 REMARK 3 8 1.5684 - 1.5000 0.95 2497 147 0.2145 0.2481 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 60.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 : 0.006 1301 REMARK 3 ANGLE : 0.995 1778 REMARK 3 CHIRALITY : 0.064 200 REMARK 3 PLANARITY : 0.004 236 REMARK 3 DIHEDRAL : 12.100 505 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 3P1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000061837. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.7L REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22272 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 37.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.770 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.66 REMARK 200 R MERGE FOR SHELL (I) : 0.77100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, MAGNESIUM CHLORIDE, SODIUM REMARK 280 CITRATE, PH 4.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.36000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.18000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.54000 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 496 REMARK 465 SER A 497 REMARK 465 ILE A 498 REMARK 465 LEU A 499 REMARK 465 SER A 668 REMARK 465 THR A 669 REMARK 465 LEU A 670 REMARK 465 LEU A 671 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 GLU A 666 -7.62 85.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 163 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 34 O REMARK 620 2 HOH A 115 O 170.7 REMARK 620 3 ASP A 524 OD1 91.4 81.7 REMARK 620 4 GLU A 562 OE2 95.3 90.9 89.5 REMARK 620 5 ASP A 583 OD1 84.5 98.1 148.9 121.5 REMARK 620 6 ASP A 583 OD2 71.5 103.2 98.8 164.4 50.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 163 DBREF 3P1G A 498 671 UNP D0UFA6 D0UFA6_9GAMR 1155 1328 SEQADV 3P1G GLY A 496 UNP D0UFA6 EXPRESSION TAG SEQADV 3P1G SER A 497 UNP D0UFA6 EXPRESSION TAG SEQADV 3P1G A UNP D0UFA6 GLY 1252 DELETION SEQADV 3P1G A UNP D0UFA6 GLU 1253 DELETION SEQADV 3P1G A UNP D0UFA6 ILE 1254 DELETION SEQADV 3P1G A UNP D0UFA6 TYR 1255 DELETION SEQADV 3P1G A UNP D0UFA6 ARG 1256 DELETION SEQADV 3P1G A UNP D0UFA6 ARG 1257 DELETION SEQADV 3P1G A UNP D0UFA6 ARG 1258 DELETION SEQADV 3P1G A UNP D0UFA6 GLY 1259 DELETION SEQADV 3P1G A UNP D0UFA6 LEU 1260 DELETION SEQADV 3P1G A UNP D0UFA6 LEU 1261 DELETION SEQADV 3P1G A UNP D0UFA6 THR 1262 DELETION SEQRES 1 A 165 GLY SER ILE LEU ALA GLU THR HIS GLY THR ARG PRO ASP SEQRES 2 A 165 LEU THR ASP GLN PRO ILE PRO ASP ALA ASP TYR THR TRP SEQRES 3 A 165 TYR THR ASP GLY SER SER PHE LEU GLN GLU GLY GLN ARG SEQRES 4 A 165 ARG ALA GLY ALA ALA VAL THR THR GLU THR GLU VAL ILE SEQRES 5 A 165 TRP ALA ARG ALA LEU PRO ALA GLY THR SER ALA GLN ARG SEQRES 6 A 165 ALA GLU LEU ILE ALA LEU THR GLN ALA LEU LYS MET ALA SEQRES 7 A 165 GLU GLY LYS LYS LEU ASN VAL TYR THR ASP SER ARG TYR SEQRES 8 A 165 ALA PHE ALA THR ALA HIS VAL HIS SER GLU GLY ARG GLU SEQRES 9 A 165 ILE LYS ASN LYS ASN GLU ILE LEU ALA LEU LEU LYS ALA SEQRES 10 A 165 LEU PHE LEU PRO LYS ARG LEU SER ILE ILE HIS CYS PRO SEQRES 11 A 165 GLY HIS GLN LYS GLY ASN SER ALA GLU ALA ARG GLY ASN SEQRES 12 A 165 ARG MET ALA ASP GLN ALA ALA ARG GLU ALA ALA MET LYS SEQRES 13 A 165 ALA VAL LEU GLU THR SER THR LEU LEU HET MG A 163 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *162(H2 O) HELIX 1 1 SER A 557 ALA A 573 1 17 HELIX 2 2 SER A 584 VAL A 593 1 10 HELIX 3 3 ASN A 613 LEU A 624 1 12 HELIX 4 4 SER A 643 LEU A 665 1 23 SHEET 1 A 5 VAL A 546 LEU A 552 0 SHEET 2 A 5 GLN A 533 THR A 541 -1 N ALA A 536 O LEU A 552 SHEET 3 A 5 TYR A 519 GLN A 530 -1 N PHE A 528 O ARG A 535 SHEET 4 A 5 LYS A 577 THR A 582 1 O TYR A 581 N THR A 523 SHEET 5 A 5 ARG A 629 HIS A 634 1 O ILE A 633 N VAL A 580 LINK O HOH A 34 MG MG A 163 1555 1555 2.59 LINK O HOH A 115 MG MG A 163 1555 1555 2.55 LINK MG MG A 163 OD1 ASP A 524 1555 1555 2.34 LINK MG MG A 163 OE2AGLU A 562 1555 1555 2.30 LINK MG MG A 163 OD1 ASP A 583 1555 1555 2.36 LINK MG MG A 163 OD2 ASP A 583 1555 1555 2.74 SITE 1 AC1 5 HOH A 34 HOH A 115 ASP A 524 GLU A 562 SITE 2 AC1 5 ASP A 583 CRYST1 37.530 37.530 100.720 90.00 90.00 90.00 P 41 4 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 0.026645 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009929 0.00000