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Yorodumi- PDB-3vq6: HIV-1 IN core domain in complex with (1-methyl-5-phenyl-1H-pyrazo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vq6 | ||||||
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Title | HIV-1 IN core domain in complex with (1-methyl-5-phenyl-1H-pyrazol-4-yl)methanol | ||||||
Components | POL polyprotein | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / RNAseH / DNA binding / DNA cleavage / DNA integration / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wielens, J. / Chalmers, D.K. / Parker, M.W. / Scanlon, M.J. | ||||||
Citation | Journal: J Biomol Screen / Year: 2013 Title: Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification? Authors: Wielens, J. / Headey, S.J. / Rhodes, D.I. / Mulder, R.J. / Dolezal, O. / Deadman, J.J. / Newman, J. / Chalmers, D.K. / Parker, M.W. / Peat, T.S. / Scanlon, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vq6.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vq6.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 3vq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/3vq6 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/3vq6 | HTTPS FTP |
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-Related structure data
Related structure data | 3vq4C 3vq5C 3vq7C 3vq8C 3vq9C 3vqaC 3vqbC 3vqcC 3vqdC 3vqeC 3vqpC 3vqqC 4ah9C 4ahrC 4ahsC 4ahtC 4ahuC 4ahvC 3l3uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17248.518 Da / Num. of mol.: 2 / Fragment: integrase core domain, UNP residues 770-927 / Mutation: C56S W131D, F139D, F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL43 / Gene: pol / Plasmid: PeT23b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72498 #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-BCK / ( | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 50mM CdCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9597 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2007 / Details: Mirror |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9597 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→61.9 Å / Num. all: 29134 / Num. obs: 29112 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3l3u Resolution: 1.8→49.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.357 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.409 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→49.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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