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- PDB-6l0c: Crystal structure of HIV-1 Integrase catalytic core domain (A128T... -

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Basic information

Entry
Database: PDB / ID: 6l0c
TitleCrystal structure of HIV-1 Integrase catalytic core domain (A128T/K173Q/F185K)
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Integrase
Function / homology
Function and homology information


DNA integration / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / 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. / Integrase core domain ...Ribonuclease H-like superfamily/Ribonuclease H / 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. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsNakamura, T. / Nakamura, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
Japan Society for the Promotion of Science Japan
CitationJournal: J.Virol. / Year: 2020
Title: A Conformational Escape Reaction of HIV-1 against an Allosteric Integrase Inhibitor.
Authors: Nakamura, T. / Nakamura, T. / Amano, M. / Miyakawa, T. / Yamagata, Y. / Matsuoka, M. / Nakata, H.
History
DepositionSep 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4367
Polymers18,9021
Non-polymers5346
Water45025
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,87114
Polymers37,8032
Non-polymers1,06812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area4640 Å2
ΔGint-121 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.769, 72.769, 64.259
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Integrase


Mass: 18901.537 Da / Num. of mol.: 1 / Mutation: A128T, K173Q, F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76353
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: sodium cacodylate, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→36.384 Å / Num. obs: 11817 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 43
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.514 / Num. unique obs: 11791

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GW6

4gw6


Resolution: 2.101→36.384 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.9
RfactorNum. reflection% reflection
Rfree0.2397 635 5.39 %
Rwork0.1948 --
obs0.1971 11791 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.77 Å2 / Biso mean: 65.2113 Å2 / Biso min: 34.05 Å2
Refinement stepCycle: final / Resolution: 2.101→36.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 22 25 1134
Biso mean--124.52 58.33 -
Num. residues----140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1012-2.26340.28471140.20062199
2.2634-2.49120.28321190.20722201
2.4912-2.85150.25591370.21772200
2.8515-3.59210.27861410.22062221
3.5921-36.3840.20571240.1772335
Refinement TLS params.Method: refined / Origin x: -38.2902 Å / Origin y: 4.9801 Å / Origin z: -2.6835 Å
111213212223313233
T0.389 Å2-0.0321 Å20.0329 Å2-0.3995 Å2-0.0224 Å2--0.3267 Å2
L1.1149 °20.2721 °20.4163 °2-5.4388 °2-0.546 °2--1.4814 °2
S0.0808 Å °-0.1644 Å °0.0356 Å °0.6488 Å °-0.1845 Å °0.0672 Å °-0.1132 Å °-0.0296 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA56 - 208
2X-RAY DIFFRACTION1allB1 - 5
3X-RAY DIFFRACTION1allS1 - 30
4X-RAY DIFFRACTION1allC1 - 2

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