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Yorodumi- PDB-1hyz: HIV INTEGRASE CORE DOMAIN COMPLEXED WITH A DERIVATIVE OF TETRAPHE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hyz | ||||||
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Title | HIV INTEGRASE CORE DOMAIN COMPLEXED WITH A DERIVATIVE OF TETRAPHENYL ARSONIUM. | ||||||
Components | INTEGRASE | ||||||
Keywords | TRANSFERASE / DNA INTEGRATION | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Molteni, V. / Greenwald, J. / Rhodes, D. / Hwang, Y. / Kwiatkowski, W. / Bushman, F.D. / Siegel, J.S. / Choe, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Identification of a small-molecule binding site at the dimer interface of the HIV integrase catalytic domain. Authors: Molteni, V. / Greenwald, J. / Rhodes, D. / Hwang, Y. / Kwiatkowski, W. / Bushman, F.D. / Siegel, J.S. / Choe, S. | ||||||
History |
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Remark 999 | Sequence The protein was expressed with N-term 6x histidine tag which when removed with thrombin ...Sequence The protein was expressed with N-term 6x histidine tag which when removed with thrombin leaves GSH at the N-terminus. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hyz.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hyz.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/1hyz ftp://data.pdbj.org/pub/pdb/validation_reports/hy/1hyz | 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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Details | Crystallographic 2-fold creates biologically relevant dimer |
-Components
#1: Protein | Mass: 18434.723 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN (RESIDUES 50-212) / Mutation: F185K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) References: UniProt: Q76353, UniProt: P12497*PLUS, RNA-directed DNA polymerase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-TTO / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, NH4SO4, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. all: 15753 / Num. obs: 15753 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.288 / % possible all: 92.6 |
Reflection shell | *PLUS % possible obs: 92.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: default for refmac
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Refinement step | Cycle: LAST / Resolution: 2.3→24 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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