HEADER VIRAL PROTEIN 18-OCT-19 6T6E TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE HIV-1 INTEGRASE TITLE 2 (PNL4-3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: POL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV, INTEGRASE, PNL4.3, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.RUFF,M.NEGRONI REVDAT 3 24-JAN-24 6T6E 1 REMARK REVDAT 2 10-FEB-21 6T6E 1 JRNL LINK REVDAT 1 22-JUL-20 6T6E 0 JRNL AUTH M.KANJA,P.CAPPY,N.LEVY,O.OLADOSU,S.SCHMIDT,P.ROSSOLILLO, JRNL AUTH 2 F.WINTER,R.GASSER,C.MOOG,M.RUFF,M.NEGRONI,D.LENER JRNL TITL NKNK: A NEW ESSENTIAL MOTIF IN THE C-TERMINAL DOMAIN OF JRNL TITL 2 HIV-1 GROUP M INTEGRASES. JRNL REF J.VIROL. V. 94 2020 JRNL REFN ESSN 1098-5514 JRNL PMID 32727879 JRNL DOI 10.1128/JVI.01035-20 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3311 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 13357 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2648 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 42.8440 - 3.4734 1.00 1268 143 0.1848 0.2084 REMARK 3 2 3.4734 - 2.7571 1.00 1252 144 0.1771 0.2003 REMARK 3 3 2.7571 - 2.4086 1.00 1283 139 0.1658 0.2459 REMARK 3 4 2.4086 - 2.1884 1.00 1245 144 0.1407 0.1711 REMARK 3 5 2.1884 - 2.0315 1.00 1296 141 0.1292 0.1779 REMARK 3 6 2.0315 - 1.9118 1.00 1234 141 0.1262 0.2182 REMARK 3 7 1.9118 - 1.8160 1.00 1264 136 0.1453 0.2273 REMARK 3 8 1.8160 - 1.7370 1.00 1306 138 0.1624 0.2427 REMARK 3 9 1.7370 - 1.6701 1.00 1219 148 0.1519 0.2669 REMARK 3 10 1.6701 - 1.6125 1.00 1273 141 0.1611 0.1971 REMARK 3 11 1.6125 - 1.5620 1.00 1290 136 0.1714 0.2061 REMARK 3 12 1.5620 - 1.5174 1.00 1246 152 0.2003 0.2676 REMARK 3 13 1.5174 - 1.4774 1.00 1252 138 0.2243 0.2873 REMARK 3 14 1.4774 - 1.4414 1.00 1246 144 0.2532 0.2830 REMARK 3 15 1.4414 - 1.4086 1.00 1285 140 0.2543 0.3146 REMARK 3 16 1.4086 - 1.3786 1.00 1255 142 0.3175 0.3387 REMARK 3 17 1.3786 - 1.3511 1.00 1268 142 0.3613 0.3890 REMARK 3 18 1.3511 - 1.3256 0.99 1247 144 0.4020 0.4077 REMARK 3 19 1.3256 - 1.3020 0.67 831 95 0.4603 0.4373 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.28 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6T6E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292104916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13357 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 42.844 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 18.60 REMARK 200 R MERGE (I) : 0.05870 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 254580.0 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 4.15100 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: PHASER REMARK 200 STARTING MODEL: 1QMC, 1IHV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 7, 0.8 M POTASSIUM REMARK 280 SODIUM TARTRATE AND 0.2 M LITHIUM SULFATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 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 19.90550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.90550 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.90550 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 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NI NI A 301 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 446 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 458 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 466 LIES ON A SPECIAL POSITION. 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 MET A 212 REMARK 465 GLY A 213 REMARK 465 HIS A 214 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 ASN A 254 -119.57 56.62 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 467 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 468 DISTANCE = 6.69 ANGSTROMS 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 NI A 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 215 NE2 REMARK 620 2 HIS A 215 NE2 0.0 REMARK 620 3 HIS A 217 NE2 91.9 91.9 REMARK 620 4 HIS A 217 NE2 91.9 91.9 0.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 301 DBREF1 6T6E A 219 270 UNP A0A290WA76_9HIV1 DBREF2 6T6E A A0A290WA76 220 271 SEQADV 6T6E MET A 212 UNP A0A290WA7 INITIATING METHIONINE SEQADV 6T6E GLY A 213 UNP A0A290WA7 EXPRESSION TAG SEQADV 6T6E HIS A 214 UNP A0A290WA7 EXPRESSION TAG SEQADV 6T6E HIS A 215 UNP A0A290WA7 EXPRESSION TAG SEQADV 6T6E HIS A 216 UNP A0A290WA7 EXPRESSION TAG SEQADV 6T6E HIS A 217 UNP A0A290WA7 EXPRESSION TAG SEQADV 6T6E HIS A 218 UNP A0A290WA7 EXPRESSION TAG SEQADV 6T6E VAL A 234 UNP A0A290WA7 ILE 235 CONFLICT SEQRES 1 A 59 MET GLY HIS HIS HIS HIS HIS HIS ILE GLN ASN PHE ARG SEQRES 2 A 59 VAL TYR TYR ARG ASP SER ARG ASP PRO VAL TRP LYS GLY SEQRES 3 A 59 PRO ALA LYS LEU LEU TRP LYS GLY GLU GLY ALA VAL VAL SEQRES 4 A 59 ILE GLN ASP ASN SER ASP ILE LYS VAL VAL PRO ARG ARG SEQRES 5 A 59 LYS ALA LYS ILE ILE ARG ASP HET NI A 301 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *68(H2 O) SHEET 1 AA1 5 ASP A 256 PRO A 261 0 SHEET 2 AA1 5 ALA A 248 ASP A 253 -1 N ASP A 253 O ASP A 256 SHEET 3 AA1 5 LYS A 236 LYS A 244 -1 N LEU A 242 O VAL A 250 SHEET 4 AA1 5 PHE A 223 TYR A 227 -1 N TYR A 227 O LYS A 236 SHEET 5 AA1 5 ALA A 265 ARG A 269 -1 O LYS A 266 N TYR A 226 LINK NE2 HIS A 215 NI NI A 301 1555 1555 2.15 LINK NE2 HIS A 215 NI NI A 301 1555 3695 2.15 LINK NE2 HIS A 217 NI NI A 301 1555 1555 2.19 LINK NE2 HIS A 217 NI NI A 301 1555 3695 2.19 CISPEP 1 GLY A 237 PRO A 238 0 6.53 SITE 1 AC1 2 HIS A 215 HIS A 217 CRYST1 49.472 49.472 39.811 90.00 90.00 120.00 P 63 6 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 0.020213 0.011670 0.000000 0.00000 SCALE2 0.000000 0.023340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025119 0.00000