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- PDB-2itg: CATALYTIC DOMAIN OF HIV-1 INTEGRASE: ORDERED ACTIVE SITE IN THE F... -

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Entry
Database: PDB / ID: 2itg
TitleCATALYTIC DOMAIN OF HIV-1 INTEGRASE: ORDERED ACTIVE SITE IN THE F185H CONSTRUCT
ComponentsHUMAN IMMUNODEFICIENCY VIRUS-1 INTEGRASE
KeywordsDNA INTEGRATION / AIDS / POLYPROTEIN / HYDROLASE / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING (VIRAL)
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral ...Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.6 Å
AuthorsBujacz, G. / Alexandratos, J. / Wlodawer, A. / Zhou-Liu, Q. / Clement-Mella, C.
Citation
Journal: FEBS Lett. / Year: 1996
Title: The catalytic domain of human immunodeficiency virus integrase: ordered active site in the F185H mutant.
Authors: Bujacz, G. / Alexandratos, J. / Qing, Z.L. / Clement-Mella, C. / Wlodawer, A.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: High-Resolution Structure of the Catalytic Domain of Avian Sarcoma Virus Integrase
Authors: Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Katz, R.A. / Skalka, A.M.
#2: Journal: Science / Year: 1994
Title: Crystal Structure of the Catalytic Domain of HIV-1 Integrase: Similarity to Other Polynucleotidyl Transferases
Authors: Dyda, F. / Hickman, A.B. / Jenkins, T.M. / Engelman, A. / Craigie, R. / Davies, D.R.
History
DepositionSep 13, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / 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_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN IMMUNODEFICIENCY VIRUS-1 INTEGRASE


Theoretical massNumber of molelcules
Total (without water)17,9211
Polymers17,9211
Non-polymers00
Water1,04558
1
A: HUMAN IMMUNODEFICIENCY VIRUS-1 INTEGRASE

A: HUMAN IMMUNODEFICIENCY VIRUS-1 INTEGRASE


Theoretical massNumber of molelcules
Total (without water)35,8432
Polymers35,8432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2360 Å2
ΔGint-16 kcal/mol
Surface area17140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.400, 72.400, 65.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein HUMAN IMMUNODEFICIENCY VIRUS-1 INTEGRASE


Mass: 17921.447 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN 50 - 212 / Mutation: F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus
Description: EXPRESSION CLONE FOR CORE, REFER TO PNAS USA, VOL. 90, PP3428-3432, APRIL 1993, AND PNAS USA, VOL. 92, PP.6057-6061, JUNE 1995
Cell line: BL21 / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12497
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.5
Details: 3-9% PEG 8000, 0.4M AMMONIUM SULFATE, 0.1M SODIUM CACODYLATE PH 6.5
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5-4 mg/mlprotein1drop
20.05 Msodium cacodylate1drop
30.2 Mammonium sulfate1drop
41.5-4.5 %PEG80001drop
50.1 Msodium cacodylate1reservoir
60.4 Mammonium sulfate1reservoir
73-9 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 5, 1996 / Details: DOUBLE FOCUSSING MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→10 Å / Num. obs: 5012 / % possible obs: 79.8 % / Observed criterion σ(I): 0 / Redundancy: 2.93 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.63
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1.38 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 1.88 / % possible all: 54.4
Reflection
*PLUS
Num. measured all: 14682
Reflection shell
*PLUS
% possible obs: 54.4 %

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1ITG

1itg


Resolution: 2.6→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.2 --
all-14682 -
obs-4400 79.8 %
Displacement parametersBiso mean: 34.16 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 0 58 1291
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0320.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0971.5
X-RAY DIFFRACTIONp_mcangle_it2.0032
X-RAY DIFFRACTIONp_scbond_it1.1232
X-RAY DIFFRACTIONp_scangle_it1.9513
X-RAY DIFFRACTIONp_plane_restr0.0130.025
X-RAY DIFFRACTIONp_chiral_restr0.1350.15
X-RAY DIFFRACTIONp_singtor_nbd0.2630.5
X-RAY DIFFRACTIONp_multtor_nbd0.3560.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.3010.5
X-RAY DIFFRACTIONp_planar_tor2.23.5
X-RAY DIFFRACTIONp_staggered_tor20.410
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.410
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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