HEADER VIRAL PROTEIN 07-NOV-17 6EX9 TITLE CRYSTAL STRUCTURE OF HIV-1 INTEGRASE CATALYTIC CORE DOMAIN WITH TITLE 2 INHIBITOR PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: INHIBITOR PEPTIDE; COMPND 7 CHAIN: B; COMPND 8 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS HIV-1, INTEGRASE, RETROVIRUSES, CATALYTIC CORE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.GALILEE,A.ALIAN REVDAT 3 17-JAN-24 6EX9 1 JRNL REVDAT 2 21-AUG-19 6EX9 1 COMPND SOURCE REVDAT 1 06-JUN-18 6EX9 0 JRNL AUTH M.GALILEE,A.ALIAN JRNL TITL MULTIMERIZATION OF HIV-1 INTEGRASE HINGES ON CONSERVED JRNL TITL 2 SH3-DOCKING PLATFORMS JRNL REF BIORXIV 2018 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/301721 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15679 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 810 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 68.2883 - 3.6595 1.00 2629 154 0.1890 0.2544 REMARK 3 2 3.6595 - 2.9046 1.00 2481 136 0.2338 0.2776 REMARK 3 3 2.9046 - 2.5374 1.00 2465 124 0.2549 0.3252 REMARK 3 4 2.5374 - 2.3054 1.00 2420 153 0.2623 0.2956 REMARK 3 5 2.3054 - 2.1402 1.00 2443 123 0.2930 0.3364 REMARK 3 6 2.1402 - 2.0140 1.00 2431 120 0.3422 0.3686 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.660 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 1201 REMARK 3 ANGLE : 0.841 1631 REMARK 3 CHIRALITY : 0.052 183 REMARK 3 PLANARITY : 0.006 206 REMARK 3 DIHEDRAL : 3.040 686 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 6EX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-16 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15682 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.014 REMARK 200 RESOLUTION RANGE LOW (A) : 68.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.88500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 1BIS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SUCCINIC ACID, 15 % W/V PEG REMARK 280 3350, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -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 -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 24.24450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.25950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.25950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.12225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.25950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.25950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.36675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.25950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.25950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 12.12225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.25950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.25950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.36675 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 24.24450 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 140 REMARK 465 ILE A 141 REMARK 465 PRO A 142 REMARK 465 TYR A 143 REMARK 465 ASN A 144 REMARK 465 PRO A 145 REMARK 465 GLN A 146 REMARK 465 SER A 147 REMARK 465 GLY A 189 REMARK 465 GLY A 190 REMARK 465 ILE A 191 REMARK 465 GLY A 192 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 GLN A 95 CG CD OE1 NE2 REMARK 470 ARG A 127 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 131 CG OD1 OD2 REMARK 470 LYS A 136 CG CD CE NZ REMARK 470 GLN A 148 CG CD OE1 NE2 REMARK 470 VAL A 151 CG1 CG2 REMARK 470 GLU A 152 CG CD OE1 OE2 REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 LYS A 186 CG CD CE NZ REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 TYR B 5 CG CD1 CD2 CE1 CE2 CZ OH 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 OD2 ASP A 202 O HOH A 301 2.18 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 PRO A 109 92.23 -68.97 REMARK 500 TYR A 194 97.51 70.87 REMARK 500 ASP A 207 8.55 -67.05 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6EX9 A 57 208 UNP A0A0U5B5J2_9HIV1 DBREF2 6EX9 A A0A0U5B5J2 57 208 DBREF 6EX9 B 1 15 PDB 6EX9 6EX9 1 15 SEQADV 6EX9 ASP A 131 UNP A0A0U5B5J TRP 131 CONFLICT SEQADV 6EX9 LYS A 185 UNP A0A0U5B5J PHE 185 CONFLICT SEQRES 1 A 152 SER PRO GLY ILE TRP GLN LEU ASP CYS THR HIS LEU GLU SEQRES 2 A 152 GLY LYS VAL ILE LEU VAL ALA VAL HIS VAL ALA SER GLY SEQRES 3 A 152 TYR ILE GLU ALA GLU VAL ILE PRO ALA GLU THR GLY GLN SEQRES 4 A 152 GLU THR ALA TYR PHE LEU LEU LYS LEU ALA GLY ARG TRP SEQRES 5 A 152 PRO VAL LYS THR ILE HIS THR ASP ASN GLY SER ASN PHE SEQRES 6 A 152 THR GLY ALA THR VAL ARG ALA ALA CYS ASP TRP ALA GLY SEQRES 7 A 152 ILE LYS GLN GLU PHE GLY ILE PRO TYR ASN PRO GLN SER SEQRES 8 A 152 GLN GLY VAL VAL GLU SER MET ASN LYS GLU LEU LYS LYS SEQRES 9 A 152 ILE ILE GLY GLN VAL ARG ASP GLN ALA GLU HIS LEU LYS SEQRES 10 A 152 THR ALA VAL GLN MET ALA VAL PHE ILE HIS ASN LYS LYS SEQRES 11 A 152 ARG LYS GLY GLY ILE GLY GLY TYR SER ALA GLY GLU ARG SEQRES 12 A 152 ILE VAL ASP ILE ILE ALA THR ASP ILE SEQRES 1 B 15 TRP SER TYR PHE TYR ASP GLY SER TYR SER TYR TYR ASP SEQRES 2 B 15 TYR GLU FORMUL 3 HOH *51(H2 O) HELIX 1 AA1 THR A 93 TRP A 108 1 16 HELIX 2 AA2 GLY A 118 GLY A 123 1 6 HELIX 3 AA3 GLY A 123 GLY A 134 1 12 HELIX 4 AA4 GLY A 149 ARG A 166 1 18 HELIX 5 AA5 ASP A 167 ALA A 169 5 3 HELIX 6 AA6 HIS A 171 LYS A 186 1 16 HELIX 7 AA7 SER A 195 ASP A 207 1 13 SHEET 1 AA1 5 ILE A 84 ILE A 89 0 SHEET 2 AA1 5 LYS A 71 HIS A 78 -1 N ALA A 76 O GLU A 85 SHEET 3 AA1 5 ILE A 60 LEU A 68 -1 N THR A 66 O ILE A 73 SHEET 4 AA1 5 THR A 112 HIS A 114 1 O HIS A 114 N LEU A 63 SHEET 5 AA1 5 LYS A 136 GLU A 138 1 O LYS A 136 N ILE A 113 SHEET 1 AA2 2 SER B 2 TYR B 3 0 SHEET 2 AA2 2 TYR B 9 SER B 10 -1 O SER B 10 N SER B 2 CRYST1 96.519 96.519 48.489 90.00 90.00 90.00 P 41 21 2 8 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 0.010361 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010361 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020623 0.00000