PDB Short entry for 2B4J HEADER VIRAL PROTEIN, RECOMBINATION 24-SEP-05 2B4J TITLE STRUCTURAL BASIS FOR THE RECOGNITION BETWEEN HIV-1 INTEGRASE AND TITLE 2 LEDGF/P75 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE (IN); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HIV-1 INTEGRASE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PC4 AND SFRS1 INTERACTING PROTEIN; COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: LEDGF; COMPND 11 SYNONYM: LENS EPITHELIUM-DERIVED GROWTH FACTOR, TRANSCRIPTIONAL COMPND 12 COACTIVATOR P75/P52, DENSE FINE SPECKLES 70 KDA PROTEIN, DFS 70, CLL- COMPND 13 ASSOCIATED ANTIGEN KW-7; COMPND 14 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 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: PSIP1, LEDGF; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PCPGST75-81 KEYWDS HIV, INTEGRATION, TRANSCRIPTION, VIRAL PROTEIN, RECOMBINATION EXPDTA X-RAY DIFFRACTION AUTHOR P.CHEREPANOV,A.L.AMBROSIO,S.RAHMAN,T.ELLENBERGER,A.ENGELMAN REVDAT 7 23-AUG-23 2B4J 1 REMARK REVDAT 6 20-OCT-21 2B4J 1 REMARK SEQADV REVDAT 5 11-OCT-17 2B4J 1 REMARK REVDAT 4 13-JUL-11 2B4J 1 VERSN REVDAT 3 24-FEB-09 2B4J 1 VERSN REVDAT 2 17-JAN-06 2B4J 1 JRNL REVDAT 1 25-OCT-05 2B4J 0 JRNL AUTH P.CHEREPANOV,A.L.AMBROSIO,S.RAHMAN,T.ELLENBERGER,A.ENGELMAN JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION BETWEEN HIV-1 INTEGRASE JRNL TITL 2 AND TRANSCRIPTIONAL COACTIVATOR P75 JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 17308 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 16260736 JRNL DOI 10.1073/PNAS.0506924102 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 32113 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 + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1627 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2223 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 35.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 1.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.184 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.106 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3584 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4819 ; 1.602 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 437 ; 5.524 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;32.690 ;25.033 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 693 ;15.922 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;19.538 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 559 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2553 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1687 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2521 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 222 ; 0.147 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.179 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.237 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2295 ; 0.981 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3564 ; 1.600 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1487 ; 2.778 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1255 ; 4.361 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 56 A 208 REMARK 3 ORIGIN FOR THE GROUP (A): 0.8516 -0.4794 -21.0989 REMARK 3 T TENSOR REMARK 3 T11: -0.0655 T22: -0.0716 REMARK 3 T33: -0.0469 T12: 0.0126 REMARK 3 T13: 0.0322 T23: 0.0744 REMARK 3 L TENSOR REMARK 3 L11: 4.4292 L22: 1.7412 REMARK 3 L33: 1.8238 L12: -0.5959 REMARK 3 L13: -1.0257 L23: 0.3917 REMARK 3 S TENSOR REMARK 3 S11: 0.2154 S12: 0.3457 S13: 0.5314 REMARK 3 S21: -0.0421 S22: -0.0868 S23: -0.0325 REMARK 3 S31: -0.1932 S32: -0.0167 S33: -0.1286 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 57 B 208 REMARK 3 ORIGIN FOR THE GROUP (A): -13.5360 -12.9638 -15.8610 REMARK 3 T TENSOR REMARK 3 T11: -0.0695 T22: -0.0585 REMARK 3 T33: -0.0106 T12: -0.0103 REMARK 3 T13: 0.0048 T23: -0.0501 REMARK 3 L TENSOR REMARK 3 L11: 4.1647 L22: 0.9899 REMARK 3 L33: 1.6376 L12: -0.3954 REMARK 3 L13: -1.3046 L23: -0.0716 REMARK 3 S TENSOR REMARK 3 S11: -0.0712 S12: 0.3343 S13: -0.3968 REMARK 3 S21: 0.0429 S22: -0.0366 S23: 0.2331 REMARK 3 S31: 0.0937 S32: -0.2525 S33: 0.1078 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 345 C 426 REMARK 3 ORIGIN FOR THE GROUP (A): -25.3205 19.5794 -4.2029 REMARK 3 T TENSOR REMARK 3 T11: -0.1407 T22: -0.1154 REMARK 3 T33: -0.1097 T12: -0.0269 REMARK 3 T13: -0.0106 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 2.2833 L22: 5.1292 REMARK 3 L33: 2.5546 L12: 0.5698 REMARK 3 L13: 0.3608 L23: 1.5667 REMARK 3 S TENSOR REMARK 3 S11: -0.2146 S12: 0.1698 S13: 0.0110 REMARK 3 S21: -0.4025 S22: 0.1793 S23: 0.2188 REMARK 3 S31: -0.0725 S32: -0.0491 S33: 0.0353 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 345 D 426 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1455 -31.5844 -18.2160 REMARK 3 T TENSOR REMARK 3 T11: -0.0328 T22: -0.0283 REMARK 3 T33: -0.1416 T12: 0.0122 REMARK 3 T13: -0.0248 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 2.6236 L22: 6.3798 REMARK 3 L33: 3.9244 L12: -1.4640 REMARK 3 L13: 0.5090 L23: -3.1630 REMARK 3 S TENSOR REMARK 3 S11: 0.1339 S12: 0.3782 S13: -0.1065 REMARK 3 S21: -0.9928 S22: -0.1260 S23: -0.0426 REMARK 3 S31: 0.4744 S32: 0.0114 S33: -0.0079 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2B4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL 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 : 32136 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY: 1BIS (INTEGRASE), 1Z9E (LEDGF) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG-3350, NA2HPO4, NAH2PO4, KH2PO4, REMARK 280 NACL, HEPES, PH 6.25, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 61.21050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.29650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.21050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.29650 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 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 47 REMARK 465 SER A 48 REMARK 465 HIS A 49 REMARK 465 MET A 50 REMARK 465 HIS A 51 REMARK 465 GLY A 52 REMARK 465 GLN A 53 REMARK 465 VAL A 54 REMARK 465 ASP A 55 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 GLN A 148 REMARK 465 GLY A 149 REMARK 465 ARG A 187 REMARK 465 LYS A 188 REMARK 465 GLY A 189 REMARK 465 GLY A 190 REMARK 465 ILE A 191 REMARK 465 GLY A 192 REMARK 465 GLY A 193 REMARK 465 TYR A 194 REMARK 465 GLN A 209 REMARK 465 THR A 210 REMARK 465 LYS A 211 REMARK 465 GLU A 212 REMARK 465 GLY B 47 REMARK 465 SER B 48 REMARK 465 HIS B 49 REMARK 465 MET B 50 REMARK 465 HIS B 51 REMARK 465 GLY B 52 REMARK 465 GLN B 53 REMARK 465 VAL B 54 REMARK 465 ASP B 55 REMARK 465 CYS B 56 REMARK 465 LYS B 188 REMARK 465 GLY B 189 REMARK 465 GLY B 190 REMARK 465 ILE B 191 REMARK 465 GLY B 192 REMARK 465 GLY B 193 REMARK 465 TYR B 194 REMARK 465 GLN B 209 REMARK 465 THR B 210 REMARK 465 LYS B 211 REMARK 465 GLU B 212 REMARK 465 PHE C 427 REMARK 465 LEU C 428 REMARK 465 VAL C 429 REMARK 465 GLY C 430 REMARK 465 GLU C 431 REMARK 465 GLY C 432 REMARK 465 ASP C 433 REMARK 465 SER C 434 REMARK 465 VAL C 435 REMARK 465 ILE C 436 REMARK 465 THR C 437 REMARK 465 GLN C 438 REMARK 465 VAL C 439 REMARK 465 LEU C 440 REMARK 465 ASN C 441 REMARK 465 LYS C 442 REMARK 465 PHE D 427 REMARK 465 LEU D 428 REMARK 465 VAL D 429 REMARK 465 GLY D 430 REMARK 465 GLU D 431 REMARK 465 GLY D 432 REMARK 465 ASP D 433 REMARK 465 SER D 434 REMARK 465 VAL D 435 REMARK 465 ILE D 436 REMARK 465 THR D 437 REMARK 465 GLN D 438 REMARK 465 VAL D 439 REMARK 465 LEU D 440 REMARK 465 ASN D 441 REMARK 465 LYS D 442 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 111 CE NZ REMARK 480 VAL A 150 CG1 CG2 REMARK 480 GLU A 152 CD OE1 OE2 REMARK 480 LYS A 156 CE NZ REMARK 480 GLU A 157 CD OE1 OE2 REMARK 480 LYS B 111 CD CE NZ REMARK 480 GLN B 146 CG CD OE1 NE2 REMARK 480 LYS B 156 CD CE NZ REMARK 480 ARG C 405 NE CZ NH1 NH2 REMARK 480 LYS D 360 NZ REMARK 480 MET D 387 CG SD CE REMARK 480 GLN D 388 CG CD OE1 NE2 REMARK 480 GLN D 391 CG CD OE1 NE2 REMARK 480 ARG D 405 CZ NH1 NH2 REMARK 480 GLN D 410 CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 102 CB - CG - CD1 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG C 404 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG C 404 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG D 404 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG D 404 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES 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 SER A 123 136.78 -39.48 REMARK 500 ASN C 367 54.13 -154.33 REMARK 500 PHE C 406 85.04 -68.87 REMARK 500 ASN D 367 56.39 -156.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 443 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 443 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z9E RELATED DB: PDB REMARK 900 LEDGF INTEGRASE-BINDING DOMAIN (RESIDUES 347-429), NMR STRUCTURE REMARK 900 RELATED ID: 1ITG RELATED DB: PDB REMARK 900 HIV-1 INTEGRASE, CATALYTIC CORE DOMAIN (RESIDUES 50-212) REMARK 900 RELATED ID: 1K6Y RELATED DB: PDB REMARK 900 HIV-1 INTEGRASE, AMINO-TERMINAL AND CATALYTIC CORE DOMAINS REMARK 900 (RESIDUES 1-212) DBREF 2B4J A 50 212 UNP P12497 POL_HV1N5 765 927 DBREF 2B4J B 50 212 UNP P12497 POL_HV1N5 765 927 DBREF 2B4J C 347 442 UNP O75475 PSIP1_HUMAN 347 442 DBREF 2B4J D 347 442 UNP O75475 PSIP1_HUMAN 347 442 SEQADV 2B4J GLY A 47 UNP P12497 CLONING ARTIFACT SEQADV 2B4J SER A 48 UNP P12497 CLONING ARTIFACT SEQADV 2B4J HIS A 49 UNP P12497 CLONING ARTIFACT SEQADV 2B4J LYS A 185 UNP P12497 PHE 900 ENGINEERED MUTATION SEQADV 2B4J GLY B 47 UNP P12497 CLONING ARTIFACT SEQADV 2B4J SER B 48 UNP P12497 CLONING ARTIFACT SEQADV 2B4J HIS B 49 UNP P12497 CLONING ARTIFACT SEQADV 2B4J LYS B 185 UNP P12497 PHE 900 ENGINEERED MUTATION SEQADV 2B4J GLY C 345 UNP O75475 CLONING ARTIFACT SEQADV 2B4J SER C 346 UNP O75475 CLONING ARTIFACT SEQADV 2B4J GLY D 345 UNP O75475 CLONING ARTIFACT SEQADV 2B4J SER D 346 UNP O75475 CLONING ARTIFACT SEQRES 1 A 166 GLY SER HIS MET HIS GLY GLN VAL ASP CYS SER PRO GLY SEQRES 2 A 166 ILE TRP GLN LEU ASP CYS THR HIS LEU GLU GLY LYS VAL SEQRES 3 A 166 ILE LEU VAL ALA VAL HIS VAL ALA SER GLY TYR ILE GLU SEQRES 4 A 166 ALA GLU VAL ILE PRO ALA GLU THR GLY GLN GLU THR ALA SEQRES 5 A 166 TYR PHE LEU LEU LYS LEU ALA GLY ARG TRP PRO VAL LYS SEQRES 6 A 166 THR VAL HIS THR ASP ASN GLY SER ASN PHE THR SER THR SEQRES 7 A 166 THR VAL LYS ALA ALA CYS TRP TRP ALA GLY ILE LYS GLN SEQRES 8 A 166 GLU PHE GLY ILE PRO TYR ASN PRO GLN SER GLN GLY VAL SEQRES 9 A 166 ILE GLU SER MET ASN LYS GLU LEU LYS LYS ILE ILE GLY SEQRES 10 A 166 GLN VAL ARG ASP GLN ALA GLU HIS LEU LYS THR ALA VAL SEQRES 11 A 166 GLN MET ALA VAL PHE ILE HIS ASN LYS LYS ARG LYS GLY SEQRES 12 A 166 GLY ILE GLY GLY TYR SER ALA GLY GLU ARG ILE VAL ASP SEQRES 13 A 166 ILE ILE ALA THR ASP ILE GLN THR LYS GLU SEQRES 1 B 166 GLY SER HIS MET HIS GLY GLN VAL ASP CYS SER PRO GLY SEQRES 2 B 166 ILE TRP GLN LEU ASP CYS THR HIS LEU GLU GLY LYS VAL SEQRES 3 B 166 ILE LEU VAL ALA VAL HIS VAL ALA SER GLY TYR ILE GLU SEQRES 4 B 166 ALA GLU VAL ILE PRO ALA GLU THR GLY GLN GLU THR ALA SEQRES 5 B 166 TYR PHE LEU LEU LYS LEU ALA GLY ARG TRP PRO VAL LYS SEQRES 6 B 166 THR VAL HIS THR ASP ASN GLY SER ASN PHE THR SER THR SEQRES 7 B 166 THR VAL LYS ALA ALA CYS TRP TRP ALA GLY ILE LYS GLN SEQRES 8 B 166 GLU PHE GLY ILE PRO TYR ASN PRO GLN SER GLN GLY VAL SEQRES 9 B 166 ILE GLU SER MET ASN LYS GLU LEU LYS LYS ILE ILE GLY SEQRES 10 B 166 GLN VAL ARG ASP GLN ALA GLU HIS LEU LYS THR ALA VAL SEQRES 11 B 166 GLN MET ALA VAL PHE ILE HIS ASN LYS LYS ARG LYS GLY SEQRES 12 B 166 GLY ILE GLY GLY TYR SER ALA GLY GLU ARG ILE VAL ASP SEQRES 13 B 166 ILE ILE ALA THR ASP ILE GLN THR LYS GLU SEQRES 1 C 98 GLY SER SER MET ASP SER ARG LEU GLN ARG ILE HIS ALA SEQRES 2 C 98 GLU ILE LYS ASN SER LEU LYS ILE ASP ASN LEU ASP VAL SEQRES 3 C 98 ASN ARG CYS ILE GLU ALA LEU ASP GLU LEU ALA SER LEU SEQRES 4 C 98 GLN VAL THR MET GLN GLN ALA GLN LYS HIS THR GLU MET SEQRES 5 C 98 ILE THR THR LEU LYS LYS ILE ARG ARG PHE LYS VAL SER SEQRES 6 C 98 GLN VAL ILE MET GLU LYS SER THR MET LEU TYR ASN LYS SEQRES 7 C 98 PHE LYS ASN MET PHE LEU VAL GLY GLU GLY ASP SER VAL SEQRES 8 C 98 ILE THR GLN VAL LEU ASN LYS SEQRES 1 D 98 GLY SER SER MET ASP SER ARG LEU GLN ARG ILE HIS ALA SEQRES 2 D 98 GLU ILE LYS ASN SER LEU LYS ILE ASP ASN LEU ASP VAL SEQRES 3 D 98 ASN ARG CYS ILE GLU ALA LEU ASP GLU LEU ALA SER LEU SEQRES 4 D 98 GLN VAL THR MET GLN GLN ALA GLN LYS HIS THR GLU MET SEQRES 5 D 98 ILE THR THR LEU LYS LYS ILE ARG ARG PHE LYS VAL SER SEQRES 6 D 98 GLN VAL ILE MET GLU LYS SER THR MET LEU TYR ASN LYS SEQRES 7 D 98 PHE LYS ASN MET PHE LEU VAL GLY GLU GLY ASP SER VAL SEQRES 8 D 98 ILE THR GLN VAL LEU ASN LYS HET PO4 A 301 5 HET GOL A 404 6 HET PO4 B 302 5 HET GOL B 403 6 HET GOL C 443 6 HET GOL D 443 6 HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 PO4 2(O4 P 3-) FORMUL 6 GOL 4(C3 H8 O3) FORMUL 11 HOH *220(H2 O) HELIX 1 1 THR A 93 TRP A 108 1 16 HELIX 2 2 GLY A 118 SER A 123 1 6 HELIX 3 3 SER A 123 GLY A 134 1 12 HELIX 4 4 VAL A 150 ARG A 166 1 17 HELIX 5 5 ASP A 167 ALA A 169 5 3 HELIX 6 6 HIS A 171 LYS A 186 1 16 HELIX 7 7 SER A 195 ILE A 208 1 14 HELIX 8 8 THR B 93 TRP B 108 1 16 HELIX 9 9 GLY B 118 SER B 123 1 6 HELIX 10 10 SER B 123 GLY B 134 1 12 HELIX 11 11 ASN B 144 ARG B 166 1 23 HELIX 12 12 ASP B 167 ALA B 169 5 3 HELIX 13 13 HIS B 171 LYS B 186 1 16 HELIX 14 14 SER B 195 ILE B 208 1 14 HELIX 15 15 SER C 346 LEU C 363 1 18 HELIX 16 16 ASP C 369 SER C 382 1 14 HELIX 17 17 THR C 386 LYS C 392 1 7 HELIX 18 18 HIS C 393 ARG C 404 1 12 HELIX 19 19 SER C 409 MET C 426 1 18 HELIX 20 20 SER D 346 LEU D 363 1 18 HELIX 21 21 ASP D 369 LEU D 383 1 15 HELIX 22 22 THR D 386 LYS D 392 1 7 HELIX 23 23 HIS D 393 ARG D 404 1 12 HELIX 24 24 SER D 409 MET D 426 1 18 SHEET 1 A 5 ILE A 84 ILE A 89 0 SHEET 2 A 5 LYS A 71 HIS A 78 -1 N ALA A 76 O GLU A 85 SHEET 3 A 5 ILE A 60 LEU A 68 -1 N ASP A 64 O VAL A 75 SHEET 4 A 5 THR A 112 HIS A 114 1 O HIS A 114 N TRP A 61 SHEET 5 A 5 LYS A 136 GLU A 138 1 O LYS A 136 N VAL A 113 SHEET 1 B 5 ILE B 84 ILE B 89 0 SHEET 2 B 5 LYS B 71 HIS B 78 -1 N ALA B 76 O GLU B 85 SHEET 3 B 5 ILE B 60 LEU B 68 -1 N GLN B 62 O VAL B 77 SHEET 4 B 5 THR B 112 THR B 115 1 O HIS B 114 N TRP B 61 SHEET 5 B 5 LYS B 136 PHE B 139 1 O GLU B 138 N VAL B 113 CISPEP 1 ILE B 141 PRO B 142 0 -7.24 SITE 1 AC1 4 THR A 66 HIS A 67 LYS A 159 LYS D 392 SITE 1 AC2 4 THR B 66 HIS B 67 LYS B 159 LYS C 392 SITE 1 AC3 6 LEU C 352 GLN C 353 HIS C 356 HIS C 393 SITE 2 AC3 6 GLU C 395 MET C 396 SITE 1 AC4 7 HOH D 36 LEU D 352 GLN D 353 HIS D 356 SITE 2 AC4 7 HIS D 393 GLU D 395 MET D 396 SITE 1 AC5 4 LYS B 71 HIS B 171 LEU B 172 HOH B 454 SITE 1 AC6 5 LYS A 71 HIS A 171 LEU A 172 HOH A 448 SITE 2 AC6 5 HOH A 458 CRYST1 122.421 60.593 71.126 90.00 109.06 90.00 C 1 2 1 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 0.008170 0.000000 0.002820 0.00000 SCALE2 0.000000 0.016500 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014880 0.00000