+Open data
-Basic information
Entry | Database: PDB / ID: 1bl3 | ||||||
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Title | CATALYTIC DOMAIN OF HIV-1 INTEGRASE | ||||||
Components | INTEGRASE | ||||||
Keywords | DNA INTEGRATION / AIDS / POLYPROTEIN / HYDROLASE / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING (VIRAL) | ||||||
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 / host cell plasma membrane / virion membrane / structural molecule activity / 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 Å | ||||||
Authors | Maignan, S. / Guilloteau, J.P. / Zhou-Liu, Q. / Clement-Mella, C. / Mikol, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. Authors: Maignan, S. / Guilloteau, J.P. / Zhou-Liu, Q. / Clement-Mella, C. / Mikol, V. #1: Journal: Science / Year: 1994 Title: Crystal Structure of the Catalytic Domain of HIV-1 Integrase: Similarity to Other Polynucleotidyl Transferases Authors: Dyda, F. / Hickman, A.B. / Jenkins, T.M. / Engelman, A. / Craigie, R. / Davies, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bl3.cif.gz | 98.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bl3.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/1bl3 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/1bl3 | HTTPS FTP |
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-Related structure data
Related structure data | 1bhlC 1bi4C 1itgS 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
#1: Protein | Mass: 17562.051 Da / Num. of mol.: 3 / Fragment: CATALYTIC CORE DOMAIN 50 - 212 / Mutation: F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12497 #2: Chemical | #3: 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: 1.92 Å3/Da / Density % sol: 36.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 435MM SODIUM CITRATE, 50MM HEPES-HCL PH 7.5, 7.5MM DTT, [PROTEIN]=0.13MM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Details: DOUBLE FOCUSSING MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 34702 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.202 / Rsym value: 0.202 / % possible all: 91.1 |
Reflection shell | *PLUS % possible obs: 91.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ITG Resolution: 2→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 34.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |