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Yorodumi- PDB-8s9q: HIV-1 Integrase Catalytic Core Domain (CCD) F185H Mutant Complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8s9q | ||||||
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Title | HIV-1 Integrase Catalytic Core Domain (CCD) F185H Mutant Complexed with STP03-0404 | ||||||
Components | Integrase | ||||||
Keywords | VIRAL PROTEIN / Integrase | ||||||
Function / homology | Function and homology information RNA stem-loop binding / DNA integration / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / zinc ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Dinh, T. / Kvaratskhelia, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: HIV-1 Integrase Catalytic Core Domain Complexed with STP-0404 Authors: Dinh, T. / Kvaratskhelia, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s9q.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s9q.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 8s9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/8s9q ftp://data.pdbj.org/pub/pdb/validation_reports/s9/8s9q | HTTPS FTP |
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-Related structure data
Related structure data | 6nujS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17921.447 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76353 |
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#2: Chemical | ChemComp-WBV / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M (NH4)2SO4, 0.1 M sodium cacodylate (pH = 6.5), 10% PEG 8000, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→31.59 Å / Num. obs: 9580 / % possible obs: 99.94 % / Redundancy: 20 % / Biso Wilson estimate: 36.03 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.05948 / Rrim(I) all: 0.2942 / Net I/σ(I): 8.67 |
Reflection shell | Resolution: 2.26→2.341 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 0.82 / Num. unique obs: 941 / CC1/2: 0.506 / CC star: 0.82 / Rpim(I) all: 0.5318 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NUJ Resolution: 2.26→31.59 Å / SU ML: 0.2927 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1506 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→31.59 Å
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Refine LS restraints |
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LS refinement shell |
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