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Yorodumi- PDB-6vka: HIV Integrase Core domain (IN) in complex with dimer-spanning ligand -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vka | ||||||
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Title | HIV Integrase Core domain (IN) in complex with dimer-spanning ligand | ||||||
Components | Integrase | ||||||
Keywords | TRANSFERASE / Virus / Inhibitor / Complex / HIV Integrase | ||||||
Function / homology | Function and homology information DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.863 Å | ||||||
Authors | Gorman, M.A. / Parker, M.W. | ||||||
Citation | Journal: To Be Published Title: HIV Integrase core domain (IN) in complex with dimeric spanning inhibitor Authors: Scanlon, M. / Gorman, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vka.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vka.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/6vka ftp://data.pdbj.org/pub/pdb/validation_reports/vk/6vka | HTTPS FTP |
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-Related 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: 18001.420 Da / Num. of mol.: 2 / Fragment: UNP residues 50-212 / Mutation: Q53E, C56S, W131E, F185K, Q209E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) References: UniProt: F2WR39, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-QZV / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.06 Å3/Da / Density % sol: 40.15 % / Description: Bi-pyramid |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 2.2 M ammonium sulfate, 200 mM potassium iodide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.96 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→46.34 Å / Num. obs: 23848 / % possible obs: 98.59 % / Redundancy: 8.6 % / Biso Wilson estimate: 22.92 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.03 / Rrim(I) all: 0.088 / Net I/av σ(I): 23.57 / Net I/σ(I): 23.57 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 3.03 / Num. unique obs: 2344 / CC1/2: 0.735 / CC star: 0.92 / Rpim(I) all: 0.277 / Rrim(I) all: 0.816 / % possible all: 96.58 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.863→46.302 Å / Cross valid method: THROUGHOUT / σ(F): 19.31 / Phase error: 30.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.863→46.302 Å
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Refine LS restraints |
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LS refinement shell |
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