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- PDB-4tsx: HIV-1 Integrase Catalytic Core Domain Mutant Complexed with Allos... -

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Basic information

Entry
Database: PDB / ID: 4tsx
TitleHIV-1 Integrase Catalytic Core Domain Mutant Complexed with Allosteric Inhibitor
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN / HIV Integrase / CCD / H171T / DDE motif / dimer interface / allosteric inhibitor / ALLINI / quinoline
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
Chem-LF0 / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.94 Å
AuthorsFeng, L. / Kvaratskhelia, M.
CitationJournal: Retrovirology / Year: 2014
Title: The mechanism of H171T resistance reveals the importance of N -protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase.
Authors: Slaughter, A. / Jurado, K.A. / Deng, N. / Feng, L. / Kessl, J.J. / Shkriabai, N. / Larue, R.C. / Fadel, H.J. / Patel, P.A. / Jena, N. / Fuchs, J.R. / Poeschla, E. / Levy, R.M. / Engelman, A. / Kvaratskhelia, M.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)18,7134
Polymers18,1151
Non-polymers5983
Water1,00956
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4268
Polymers36,2312
Non-polymers1,1956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area3910 Å2
ΔGint-63 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.248, 72.248, 66.032
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsFunctional biological unit is the tetramer of full length protein

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Components

#1: Protein Integrase


Mass: 18115.402 Da / Num. of mol.: 1 / Fragment: Catalytical core Domain, UNP residues 50-212 / Mutation: H171T, F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F2WR39
#2: Chemical ChemComp-LF0 / (2S)-tert-butoxy[4-(3,4-dihydro-2H-chromen-6-yl)-2-methylquinolin-3-yl]ethanoic acid


Mass: 405.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.75 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 277.5 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG8000, 0.1 M Na Cacodylate, pH 6.5, 0.1 M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 24, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 15117 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.054 / Χ2: 2.431 / Net I/av σ(I): 48.449 / Net I/σ(I): 24.9 / Num. measured all: 73892
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.94-1.974.80.4454.227311.476100
1.97-2.014.80.3827641.542100
2.01-2.054.80.3397301.614100
2.05-2.094.80.2947501.777100
2.09-2.144.90.2497421.798100
2.14-2.184.90.1997431.915100
2.18-2.244.90.1817412.00399.7
2.24-2.34.90.157492.242100
2.3-2.374.90.1367502.125100
2.37-2.444.90.1227602.31100
2.44-2.534.90.1057372.59299.9
2.53-2.634.90.0937532.675100
2.63-2.754.90.0817452.768100
2.75-2.950.0697622.84199.7
2.9-3.0850.0627453.16699.7
3.08-3.324.90.0547693.14399.9
3.32-3.6550.0467593.21100
3.65-4.184.90.0457753.11299.9
4.18-5.264.90.0437783.027100
5.26-504.60.0398343.02599.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
SCALEPACKdata scaling
RefinementResolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2264 / WRfactor Rwork: 0.191 / FOM work R set: 0.8455 / SU B: 3.151 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1421 / SU Rfree: 0.1338 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1517 10.1 %RANDOM
Rwork0.1899 13530 --
obs0.1931 15047 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134 Å2 / Biso mean: 46.193 Å2 / Biso min: 25.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: final / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 40 56 1212
Biso mean--49.64 52.34 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191185
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9881599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1045140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8612546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.97115197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.515154
X-RAY DIFFRACTIONr_chiral_restr0.1420.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021846
X-RAY DIFFRACTIONr_mcbond_it3.614.414578
X-RAY DIFFRACTIONr_mcangle_it5.5466.544712
X-RAY DIFFRACTIONr_scbond_it4.174.668607
LS refinement shellResolution: 1.94→1.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 127 -
Rwork0.244 969 -
all-1096 -
obs--99.55 %

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