HEADER HYDROLASE 09-DEC-11 3V1Q TITLE CRYSTAL STRUCTURES OF THE REVERSE TRANSCRIPTASE-ASSOCIATED TITLE 2 RIBONUCLEASE H DOMAIN OF XENOTROPIC MURINE LEUKEMIA-VIRUS RELATED TITLE 3 VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE TRANSCRIPTASE/RIBONUCLEASE H P80; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNASE H DOMAIN (UNP RESIDUES 1155-1328); COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOTROPIC MULV-RELATED VIRUS VP35; SOURCE 3 ORGANISM_COMMON: XMRV; SOURCE 4 ORGANISM_TAXID: 356663; SOURCE 5 GENE: GAG-POL, POL_XMRV3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS REVERSE TRANSCRIPTION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.ZHOU,A.WLODAWER REVDAT 3 28-FEB-24 3V1Q 1 SEQADV REVDAT 2 28-MAR-12 3V1Q 1 JRNL REVDAT 1 14-MAR-12 3V1Q 0 JRNL AUTH D.ZHOU,S.CHUNG,M.MILLER,S.F.LE GRICE,A.WLODAWER JRNL TITL CRYSTAL STRUCTURES OF THE REVERSE TRANSCRIPTASE-ASSOCIATED JRNL TITL 2 RIBONUCLEASE H DOMAIN OF XENOTROPIC MURINE LEUKEMIA-VIRUS JRNL TITL 3 RELATED VIRUS. JRNL REF J.STRUCT.BIOL. V. 177 638 2012 JRNL REFN ISSN 1047-8477 JRNL PMID 22366278 JRNL DOI 10.1016/J.JSB.2012.02.006 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9334 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 747 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 18.4433 - 3.4142 1.00 1731 151 0.1445 0.1532 REMARK 3 2 3.4142 - 2.7127 1.00 1710 149 0.1652 0.2141 REMARK 3 3 2.7127 - 2.3706 1.00 1722 150 0.1826 0.2514 REMARK 3 4 2.3706 - 2.1543 1.00 1713 149 0.2111 0.2406 REMARK 3 5 2.1543 - 2.0000 1.00 1711 148 0.2461 0.2628 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 60.39 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.090 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) : -0.60800 REMARK 3 B22 (A**2) : -0.60800 REMARK 3 B33 (A**2) : 2.77040 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 : 0.015 1228 REMARK 3 ANGLE : 1.561 1661 REMARK 3 CHIRALITY : 0.113 186 REMARK 3 PLANARITY : 0.008 218 REMARK 3 DIHEDRAL : 15.463 456 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 9.8876 10.4595 -6.0221 REMARK 3 T TENSOR REMARK 3 T11: 0.1208 T22: 0.1217 REMARK 3 T33: 0.0959 T12: 0.0139 REMARK 3 T13: 0.0157 T23: -0.0133 REMARK 3 L TENSOR REMARK 3 L11: 0.8753 L22: 2.3617 REMARK 3 L33: 0.4447 L12: 0.7073 REMARK 3 L13: 0.3371 L23: 0.1795 REMARK 3 S TENSOR REMARK 3 S11: 0.0161 S12: 0.0503 S13: -0.1068 REMARK 3 S21: -0.0322 S22: 0.0136 S23: -0.0424 REMARK 3 S31: -0.0261 S32: 0.0384 S33: 0.0000 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 3V1Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9361 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.14600 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.710 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 (%): 36.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG1500, 5 MM MAGNESIUM CHLORIDE, REMARK 280 100 MM SODIUM CITRATE, PH 4.7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 49.95500 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 24.97750 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 74.93250 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 494 REMARK 465 ILE A 495 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: 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 OE2 GLU A 610 O HOH A 715 1.73 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 HIS A 503 29.87 48.47 REMARK 500 THR A 505 -62.07 -102.56 REMARK 500 GLU A 666 -16.01 78.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3V1O RELATED DB: PDB REMARK 900 RELATED ID: 3V1R RELATED DB: PDB DBREF 3V1Q A 498 671 UNP Q2F7J3 POL_XMRV3 1155 1328 SEQADV 3V1Q GLY A 494 UNP Q2F7J3 EXPRESSION TAG SEQADV 3V1Q ILE A 495 UNP Q2F7J3 EXPRESSION TAG SEQADV 3V1Q GLY A 496 UNP Q2F7J3 EXPRESSION TAG SEQADV 3V1Q SER A 497 UNP Q2F7J3 EXPRESSION TAG SEQADV 3V1Q A UNP Q2F7J3 GLY 1252 DELETION SEQADV 3V1Q A UNP Q2F7J3 GLU 1253 DELETION SEQADV 3V1Q A UNP Q2F7J3 ILE 1254 DELETION SEQADV 3V1Q A UNP Q2F7J3 TYR 1255 DELETION SEQADV 3V1Q A UNP Q2F7J3 ARG 1256 DELETION SEQADV 3V1Q A UNP Q2F7J3 ARG 1257 DELETION SEQADV 3V1Q A UNP Q2F7J3 ARG 1258 DELETION SEQADV 3V1Q A UNP Q2F7J3 GLY 1259 DELETION SEQADV 3V1Q A UNP Q2F7J3 LEU 1260 DELETION SEQADV 3V1Q A UNP Q2F7J3 LEU 1261 DELETION SEQADV 3V1Q A UNP Q2F7J3 THR 1262 DELETION SEQRES 1 A 167 GLY ILE GLY SER ILE LEU ALA GLU THR HIS GLY THR ARG SEQRES 2 A 167 PRO ASP LEU THR ASP GLN PRO ILE PRO ASP ALA ASP TYR SEQRES 3 A 167 THR TRP TYR THR ASP GLY SER SER PHE LEU GLN GLU GLY SEQRES 4 A 167 GLN ARG ARG ALA GLY ALA ALA VAL THR THR GLU THR GLU SEQRES 5 A 167 VAL ILE TRP ALA ARG ALA LEU PRO ALA GLY THR SER ALA SEQRES 6 A 167 GLN ARG ALA GLU LEU ILE ALA LEU THR GLN ALA LEU LYS SEQRES 7 A 167 MET ALA GLU GLY LYS LYS LEU ASN VAL TYR THR ASP SER SEQRES 8 A 167 ARG TYR ALA PHE ALA THR ALA HIS VAL HIS SER GLU GLY SEQRES 9 A 167 ARG GLU ILE LYS ASN LYS ASN GLU ILE LEU ALA LEU LEU SEQRES 10 A 167 LYS ALA LEU PHE LEU PRO LYS ARG LEU SER ILE ILE HIS SEQRES 11 A 167 CYS PRO GLY HIS GLN LYS GLY ASN SER ALA GLU ALA ARG SEQRES 12 A 167 GLY ASN ARG MET ALA ASP GLN ALA ALA ARG GLU ALA ALA SEQRES 13 A 167 MET LYS ALA VAL LEU GLU THR SER THR LEU LEU FORMUL 2 HOH *80(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 TRP A 521 SHEET 5 A 5 ARG A 629 HIS A 634 1 O ILE A 633 N VAL A 580 CRYST1 37.530 37.530 99.910 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 0.010009 0.00000