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Open data
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Basic information
Entry | Database: PDB / ID: 1bi4 | ||||||
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Title | CATALYTIC DOMAIN OF HIV-1 INTEGRASE | ||||||
![]() | (INTEGRASE) x 2 | ||||||
![]() | DNA INTEGRATION / AIDS / POLYPROTEIN / HYDROLASE / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING (VIRAL) | ||||||
Function / homology | ![]() HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Maignan, S. / Guilloteau, J.P. / Zhou-Liu, Q. / Clement-Mella, C. / Mikol, V. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.9 KB | Display | ![]() |
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PDB format | ![]() | 76.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.7 KB | Display | ![]() |
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Full document | ![]() | 386.6 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bhlC ![]() 1bl3C ![]() 1itgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17562.051 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE DOMAIN 50 - 212 / Mutation: F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: REFERENCE, PNAS USA, VOL. 90, PP 3428-3432, AND PNAS USA 92, PP. 6057-6061 Cell line: BL21 / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Protein | | Mass: 17576.078 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN 50 - 212 / Mutation: F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: REFERENCE, PNAS USA, VOL. 90, PP 3428-3432, AND PNAS USA 92, PP. 6057-6061 Cell line: BL21 / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 435 MM SODIUM CITRATE, 50 MM HEPES-HCL, PH 7.5, 7.5 MM DTT, PROTEIN CONCENTRATION, 0.13 MM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 21, 1996 / 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: 2.2→15 Å / Num. obs: 10359 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 7.3 / Rsym value: 0.153 / % possible all: 93.7 |
Reflection | *PLUS Num. obs: 19078 / % possible obs: 96.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 95.2 % / Rmerge(I) obs: 0.246 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ITG Resolution: 2.5→15 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: 39.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |