HEADER HYDROLASE 14-AUG-15 5D7U TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF MMTV INTEGRASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PR160; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, UNP RESIDUES 1645-1702; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MOUSE MAMMARY TUMOR VIRUS; SOURCE 3 ORGANISM_COMMON: MMTV; SOURCE 4 ORGANISM_TAXID: 11757; SOURCE 5 GENE: GAG-PRO-POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET20B(+) KEYWDS INTEGRASE, POL, RETROVIRUS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.J.COOK,V.E.PYE,A.BALLANDRAS-COLAS,A.ENGELMAN,P.CHEREPANOV REVDAT 4 10-JAN-24 5D7U 1 REMARK REVDAT 3 02-MAR-16 5D7U 1 JRNL REVDAT 2 24-FEB-16 5D7U 1 JRNL REVDAT 1 17-FEB-16 5D7U 0 JRNL AUTH A.BALLANDRAS-COLAS,M.BROWN,N.J.COOK,T.G.DEWDNEY,B.DEMELER, JRNL AUTH 2 P.CHEREPANOV,D.LYUMKIS,A.N.ENGELMAN JRNL TITL CRYO-EM REVEALS A NOVEL OCTAMERIC INTEGRASE STRUCTURE FOR JRNL TITL 2 BETARETROVIRAL INTASOME FUNCTION. JRNL REF NATURE V. 530 358 2016 JRNL REFN ESSN 1476-4687 JRNL PMID 26887496 JRNL DOI 10.1038/NATURE16955 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10PRE_2091: ???) 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) : 34.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 870 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 34.7811 - 2.7253 1.00 2891 164 0.1654 0.2110 REMARK 3 2 2.7253 - 2.1633 1.00 2776 148 0.1786 0.2083 REMARK 3 3 2.1633 - 1.8898 1.00 2763 128 0.1297 0.1695 REMARK 3 4 1.8898 - 1.7171 1.00 2757 129 0.1288 0.2033 REMARK 3 5 1.7171 - 1.5940 1.00 2740 138 0.1427 0.2284 REMARK 3 6 1.5940 - 1.5000 0.99 2651 163 0.1536 0.2384 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.900 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 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 : 0.007 931 REMARK 3 ANGLE : 1.048 1282 REMARK 3 CHIRALITY : 0.068 135 REMARK 3 PLANARITY : 0.007 162 REMARK 3 DIHEDRAL : 13.534 565 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 5D7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212801. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17494 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 46.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.2000 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) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 0.58500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 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: 1EX4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% ISOPROPANOL, 0.2M AMMONIUM REMARK 280 ACETATE, 0.1M HEPES, PH7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 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 69.54350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.54350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 17.99400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.13950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.99400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.13950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.54350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.99400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 21.13950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.54350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.99400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 21.13950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 209 REMARK 465 PRO A 210 REMARK 465 GLY A 211 REMARK 465 SER A 212 REMARK 465 GLU A 266 REMARK 465 GLY B 209 REMARK 465 PRO B 210 REMARK 465 GLY B 211 REMARK 465 SER B 212 REMARK 465 ALA B 213 REMARK 465 ASP B 214 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 O2 IPA B 301 O HOH B 401 2.01 REMARK 500 O2 IPA A 301 O HOH A 401 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 433 O HOH B 433 3555 2.14 REMARK 500 O HOH A 408 O HOH A 408 4555 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 433 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 434 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH B 445 DISTANCE = 8.63 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPA B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CZ1 RELATED DB: PDB REMARK 900 FRAGMENT OF THE SAME PROTEIN REMARK 900 RELATED ID: 5CZ2 RELATED DB: PDB REMARK 900 FRAGMENT OF THE SAME PROTEIN REMARK 900 RELATED ID: 1EX4 RELATED DB: PDB REMARK 900 MOLECULAR REPLACEMENT SEARCH MODEL DBREF 5D7U A 209 266 UNP O56220 O56220_MMTV 1645 1702 DBREF 5D7U B 209 266 UNP O56220 O56220_MMTV 1645 1702 SEQADV 5D7U GLY A 211 UNP O56220 ILE 1647 CONFLICT SEQADV 5D7U SER A 252 UNP O56220 THR 1688 CONFLICT SEQADV 5D7U GLY B 211 UNP O56220 ILE 1647 CONFLICT SEQADV 5D7U SER B 252 UNP O56220 THR 1688 CONFLICT SEQRES 1 A 58 GLY PRO GLY SER ALA ASP PRO LYS PRO MET VAL MET TRP SEQRES 2 A 58 LYS ASP LEU LEU THR GLY SER TRP LYS GLY PRO ASP VAL SEQRES 3 A 58 LEU ILE THR ALA GLY ARG GLY TYR ALA CYS VAL PHE PRO SEQRES 4 A 58 GLN ASP ALA GLU SER PRO ILE TRP VAL PRO ASP ARG PHE SEQRES 5 A 58 ILE ARG PRO PHE THR GLU SEQRES 1 B 58 GLY PRO GLY SER ALA ASP PRO LYS PRO MET VAL MET TRP SEQRES 2 B 58 LYS ASP LEU LEU THR GLY SER TRP LYS GLY PRO ASP VAL SEQRES 3 B 58 LEU ILE THR ALA GLY ARG GLY TYR ALA CYS VAL PHE PRO SEQRES 4 B 58 GLN ASP ALA GLU SER PRO ILE TRP VAL PRO ASP ARG PHE SEQRES 5 B 58 ILE ARG PRO PHE THR GLU HET IPA A 301 4 HET IPA B 301 4 HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 3 IPA 2(C3 H8 O) FORMUL 5 HOH *79(H2 O) SHEET 1 AA1 5 ILE A 254 PRO A 257 0 SHEET 2 AA1 5 TYR A 242 VAL A 245 -1 N VAL A 245 O ILE A 254 SHEET 3 AA1 5 TRP A 229 GLY A 239 -1 N ILE A 236 O CYS A 244 SHEET 4 AA1 5 MET A 218 LYS A 222 -1 N TRP A 221 O LYS A 230 SHEET 5 AA1 5 ILE A 261 PHE A 264 -1 O ARG A 262 N MET A 220 SHEET 1 AA2 5 ILE B 254 PRO B 257 0 SHEET 2 AA2 5 TYR B 242 VAL B 245 -1 N VAL B 245 O ILE B 254 SHEET 3 AA2 5 TRP B 229 GLY B 239 -1 N ILE B 236 O CYS B 244 SHEET 4 AA2 5 MET B 218 LYS B 222 -1 N TRP B 221 O LYS B 230 SHEET 5 AA2 5 ILE B 261 PHE B 264 -1 O ARG B 262 N MET B 220 CISPEP 1 ASP A 214 PRO A 215 0 -1.54 CISPEP 2 GLY A 231 PRO A 232 0 2.08 CISPEP 3 GLY B 231 PRO B 232 0 2.61 SITE 1 AC1 4 LEU A 224 HOH A 401 THR B 237 GLY B 239 SITE 1 AC2 5 THR A 237 GLY A 239 ASP B 223 LEU B 224 SITE 2 AC2 5 HOH B 401 CRYST1 35.988 42.279 139.087 90.00 90.00 90.00 C 2 2 21 16 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 0.027787 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007190 0.00000