HEADER HYDROLASE 13-JUN-06 2HB5 TITLE CRYSTAL STRUCTURE OF THE MOLONEY MURINE LEUKEMIA VIRUS RNASE H DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE TRANSCRIPTASE/RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNASE H DOMAIN (RESIDUES 618-791); COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MOLONEY MURINE LEUKEMIA VIRUS; SOURCE 3 ORGANISM_TAXID: 11801; SOURCE 4 GENE: POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNASE H, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.LIM,G.G.GREGORIO,C.A.BINGMAN,E.MARTINEZ-HACKERT,W.A.HENDRICKSON, AUTHOR 2 S.P.GOFF REVDAT 5 16-OCT-24 2HB5 1 REMARK REVDAT 4 22-MAR-23 2HB5 1 AUTHOR JRNL REMARK SEQADV REVDAT 4 2 1 LINK REVDAT 3 18-OCT-17 2HB5 1 REMARK REVDAT 2 24-FEB-09 2HB5 1 VERSN REVDAT 1 29-AUG-06 2HB5 0 JRNL AUTH D.LIM,G.G.GREGORIO,C.A.BINGMAN,E.MARTINEZ-HACKERT, JRNL AUTH 2 W.A.HENDRICKSON,S.P.GOFF JRNL TITL CRYSTAL STRUCTURE OF THE MOLONEY MURINE LEUKEMIA VIRUS RNASE JRNL TITL 2 H DOMAIN. JRNL REF J.VIROL. V. 80 8379 2006 JRNL REFN ISSN 0022-538X JRNL PMID 16912289 JRNL DOI 10.1128/JVI.00750-06 REMARK 2 REMARK 2 RESOLUTION. 1.59 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.66 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) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 15825 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) : 0.196 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1593 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL 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 : 1133 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 148 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.261 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 2HB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038154. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98793, 0.97938, 0.97908, REMARK 200 0.96866 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15825 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 21.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4000, 0.1M AMMONIUM SULFATE, REMARK 280 150MM NACL, 1.25%PEG-MME 550, 1% 2-PROPANOL, 0.5MM ZINC SULFATE, REMARK 280 5MM MES , PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 1 REMARK 465 ILE A 2 REMARK 465 LEU A 3 REMARK 465 ALA A 4 REMARK 465 GLU A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 129 REMARK 465 GLY A 130 REMARK 465 HIS A 131 REMARK 465 GLN A 132 REMARK 465 LYS A 133 REMARK 465 THR A 162 REMARK 465 LEU A 163 REMARK 465 LEU A 164 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 HIS A 7 CB CG ND1 CD2 CE1 NE2 REMARK 470 THR A 160 OG1 CG2 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 200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 28 OD2 REMARK 620 2 GLU A 66 OE2 110.8 REMARK 620 3 ASP A 87 OD2 108.1 100.6 REMARK 620 4 ASP A 87 OD1 86.1 151.3 51.2 REMARK 620 5 HOH A 202 O 67.3 137.5 120.8 69.8 REMARK 620 6 HOH A 203 O 75.6 76.9 176.2 131.0 61.3 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 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 201 DBREF 2HB5 A 2 164 UNP P03355 POL_MLVMO 618 791 SEQADV 2HB5 GLY A 1 UNP P03355 CLONING ARTIFACT SEQADV 2HB5 MSE A 76 UNP P03355 MET 692 MODIFIED RESIDUE SEQADV 2HB5 A UNP P03355 ILE 713 DELETION SEQADV 2HB5 A UNP P03355 HIS 714 DELETION SEQADV 2HB5 A UNP P03355 GLY 715 DELETION SEQADV 2HB5 A UNP P03355 GLU 716 DELETION SEQADV 2HB5 A UNP P03355 ILE 717 DELETION SEQADV 2HB5 A UNP P03355 TYR 718 DELETION SEQADV 2HB5 A UNP P03355 ARG 719 DELETION SEQADV 2HB5 A UNP P03355 ARG 720 DELETION SEQADV 2HB5 A UNP P03355 ARG 721 DELETION SEQADV 2HB5 A UNP P03355 GLY 722 DELETION SEQADV 2HB5 A UNP P03355 LEU 723 DELETION SEQADV 2HB5 MSE A 144 UNP P03355 MET 771 MODIFIED RESIDUE SEQRES 1 A 164 GLY ILE LEU ALA GLU ALA HIS GLY THR ARG PRO ASP LEU SEQRES 2 A 164 THR ASP GLN PRO LEU PRO ASP ALA ASP HIS THR TRP TYR SEQRES 3 A 164 THR ASP GLY SER SER LEU LEU GLN GLU GLY GLN ARG LYS SEQRES 4 A 164 ALA GLY ALA ALA VAL THR THR GLU THR GLU VAL ILE TRP SEQRES 5 A 164 ALA LYS ALA LEU PRO ALA GLY THR SER ALA GLN ARG ALA SEQRES 6 A 164 GLU LEU ILE ALA LEU THR GLN ALA LEU LYS MSE ALA GLU SEQRES 7 A 164 GLY LYS LYS LEU ASN VAL TYR THR ASP SER ARG TYR ALA SEQRES 8 A 164 PHE ALA THR ALA HIS LEU THR SER GLU GLY LYS GLU ILE SEQRES 9 A 164 LYS ASN LYS ASP GLU ILE LEU ALA LEU LEU LYS ALA LEU SEQRES 10 A 164 PHE LEU PRO LYS ARG LEU SER ILE ILE HIS CYS PRO GLY SEQRES 11 A 164 HIS GLN LYS GLY HIS SER ALA GLU ALA ARG GLY ASN ARG SEQRES 12 A 164 MSE ALA ASP GLN ALA ALA ARG LYS ALA ALA ILE THR GLU SEQRES 13 A 164 THR PRO ASP THR SER THR LEU LEU MODRES 2HB5 MSE A 76 MET SELENOMETHIONINE MODRES 2HB5 MSE A 144 MET SELENOMETHIONINE HET MSE A 76 8 HET MSE A 144 8 HET MG A 200 1 HET SO4 A 201 5 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 MG MG 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *148(H2 O) HELIX 1 1 SER A 61 ALA A 77 1 17 HELIX 2 2 SER A 88 ALA A 95 1 8 HELIX 3 3 ASN A 106 LEU A 117 1 12 HELIX 4 4 SER A 136 GLU A 156 1 21 SHEET 1 A 5 VAL A 50 LEU A 56 0 SHEET 2 A 5 GLN A 37 THR A 45 -1 N VAL A 44 O TRP A 52 SHEET 3 A 5 HIS A 23 GLN A 34 -1 N SER A 30 O GLY A 41 SHEET 4 A 5 LYS A 81 THR A 86 1 O TYR A 85 N TRP A 25 SHEET 5 A 5 ARG A 122 HIS A 127 1 O ILE A 126 N VAL A 84 LINK C ALYS A 75 N MSE A 76 1555 1555 1.33 LINK C BLYS A 75 N MSE A 76 1555 1555 1.33 LINK C MSE A 76 N ALA A 77 1555 1555 1.33 LINK C ARG A 143 N MSE A 144 1555 1555 1.33 LINK C MSE A 144 N ALA A 145 1555 1555 1.33 LINK OD2 ASP A 28 MG MG A 200 1555 1555 2.41 LINK OE2AGLU A 66 MG MG A 200 1555 1555 2.38 LINK OD2 ASP A 87 MG MG A 200 1555 1555 2.02 LINK OD1 ASP A 87 MG MG A 200 1555 1555 2.80 LINK MG MG A 200 O HOH A 202 1555 1555 2.50 LINK MG MG A 200 O HOH A 203 1555 1555 2.60 SITE 1 AC1 5 ASP A 28 GLU A 66 ASP A 87 HOH A 202 SITE 2 AC1 5 HOH A 203 SITE 1 AC2 10 ARG A 64 LYS A 105 ASN A 106 LYS A 107 SITE 2 AC2 10 GLY A 134 HIS A 135 SER A 136 HOH A 204 SITE 3 AC2 10 HOH A 229 HOH A 323 CRYST1 32.326 34.107 34.802 78.21 69.85 64.79 P 1 1 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 0.030935 -0.014563 -0.010387 0.00000 SCALE2 0.000000 0.032406 -0.002203 0.00000 SCALE3 0.000000 0.000000 0.030678 0.00000