+Open data
-Basic information
Entry | Database: PDB / ID: 1k6y | ||||||
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Title | Crystal Structure of a Two-Domain Fragment of HIV-1 Integrase | ||||||
Components | Integrase | ||||||
Keywords | TRANSFERASE / HIV-1 / integrase / domain organization | ||||||
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wang, J. / Ling, H. / Yang, W. / Craigie, R. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein. Authors: Wang, J.Y. / Ling, H. / Yang, W. / Craigie, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k6y.cif.gz | 159.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k6y.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/1k6y ftp://data.pdbj.org/pub/pdb/validation_reports/k6/1k6y | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 23319.490 Da / Num. of mol.: 4 / Fragment: N-terminal and core domains (Residues 716-927) / Mutation: F185K, W131D, F139D 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: Q72498, UniProt: P12497*PLUS, RNA-directed DNA polymerase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-PO4 / #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: 3.97 Å3/Da / Density % sol: 68.99 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6 Details: 0.7 M NaH2PO4/1.0 K2HPO4, 0.1M Na acetate, pH 6.0, VAPOR DIFFUSION, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.2827 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 8, 2001 / Details: mirrors |
Radiation | Monochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2827 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 59673 / Num. obs: 51553 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 |
Reflection shell | Resolution: 2.4→2.44 Å / % possible all: 84.4 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Num. obs: 53869 / % possible obs: 90.1 % / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 84.4 % / Rmerge(I) obs: 0.356 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.8 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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