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- PDB-1ihv: SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF HIV-1 INTEGRASE, ... -

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Basic information

Entry
Database: PDB / ID: 1ihv
TitleSOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF HIV-1 INTEGRASE, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsHIV-1 INTEGRASE
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / AIDS / POLYPROTEIN
Function / homology
Function and homology information


nucleotidyltransferase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / symbiont entry into host cell / symbiont-mediated suppression of host gene expression ...nucleotidyltransferase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / DNA binding / metal ion binding
Similarity search - Function
Integrase, C-terminal domain superfamily, retroviral / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / Ribonuclease H superfamily / Ribonuclease H-like superfamily ...Integrase, C-terminal domain superfamily, retroviral / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR
AuthorsClore, G.M. / Lodi, P.J. / Ernst, J.A. / Gronenborn, A.M.
CitationJournal: Biochemistry / Year: 1995
Title: Solution structure of the DNA binding domain of HIV-1 integrase.
Authors: Lodi, P.J. / Ernst, J.A. / Kuszewski, J. / Hickman, A.B. / Engelman, A. / Craigie, R. / Clore, G.M. / Gronenborn, A.M.
History
DepositionMay 12, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 INTEGRASE
B: HIV-1 INTEGRASE


Theoretical massNumber of molelcules
Total (without water)12,2782
Polymers12,2782
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: Protein HIV-1 INTEGRASE


Mass: 6139.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P04586

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM XPLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM XPLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92 - 96) AND 1H CHEMICAL SHIFT (KUSZEWSKI ET AL., 1995 J. MAGN RESON. SERIES B IN PRESS) RESTRAINTS. THE 3D STRUCTURE OF HIV-1 INTEGRASE SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 2386 EXPERIMENTAL RESTRAINTS (FOR THE DIMER): (A) INTRASUBUNIT: 332 SEQUENTIAL (|I-J|=1), 202 MEDIUM RANGE (1 < |I-J| >=5) AND 530 LONG RANGE (|I-J| >5) INTERRESIDUES 318 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 74 DISTANCE RESTRAINTS FOR 37 HYDROGEN BONDS; 192 TORSION ANGLE (98 PHI, 20 PSI, 50 CHI1 AND 24 CHI2) RESTRAINTS; 78 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; 194 (100 CALPHA AND 94 CBETA) 13C SHIFT RESTRAINTS; AND 392 1H CHEMICAL SHIFT RESTRAINTS (102 CAH, 52 METHYL AND 238 OTHERS). (B) 44 INTERSUBUNIT INTERPROTON DISTANCE RESTRAINTS (C) 30 AMBIGUOUS INTERPROTON DISTANCE RESTRAINTS THAT CAN ARISE FROM INTRA AND/OR INTERSUBUNIT INTERACTIONS. THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED MEAN STRUCTURE AND THE LAST COLUMN REPRESENTS THE RMS OF THE 40 INDIVIDUAL SIMULATED ANNEALING STRUCTURES FOUND IN PDB ENTRY 1IHW ABOUT THE MEAN COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers submitted total number: 1

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