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Yorodumi- PDB-3vqp: HIV-1 IN core domain in complex with 2,3-dihydro-1,4-benzodioxin-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vqp | ||||||
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Title | HIV-1 IN core domain in complex with 2,3-dihydro-1,4-benzodioxin-5-ylmethanol | ||||||
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 stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / 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: 2.1 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 | 3vqp.cif.gz | 70.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vqp.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vqp_validation.pdf.gz | 468.3 KB | Display | wwPDB validaton report |
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Full document | 3vqp_full_validation.pdf.gz | 474.6 KB | Display | |
Data in XML | 3vqp_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 3vqp_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/3vqp ftp://data.pdbj.org/pub/pdb/validation_reports/vq/3vqp | HTTPS FTP |
-Related structure data
Related structure data | 3vq4C 3vq5C 3vq6C 3vq7C 3vq8C 3vq9C 3vqaC 3vqbC 3vqcC 3vqdC 3vqeC 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 55 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | ChemComp-DBJ / | #6: 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: 2.29 Å3/Da / Density % sol: 46.25 % |
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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-B / Wavelength: 0.97949 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2007 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 19014 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Rsym value: 0.083 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.09→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5435 / Rsym value: 0.398 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3l3u Resolution: 2.1→41.06 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.129 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.177 / 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: 41.065 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→41.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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