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- PDB-2itg: CATALYTIC DOMAIN OF HIV-1 INTEGRASE: ORDERED ACTIVE SITE IN THE F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2itg | ||||||
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Title | CATALYTIC DOMAIN OF HIV-1 INTEGRASE: ORDERED ACTIVE SITE IN THE F185H CONSTRUCT | ||||||
![]() | HUMAN IMMUNODEFICIENCY VIRUS-1 INTEGRASE | ||||||
![]() | 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 | ![]() ![]() | ||||||
![]() | Bujacz, G. / Alexandratos, J. / Wlodawer, A. / Zhou-Liu, Q. / Clement-Mella, C. | ||||||
![]() | ![]() Title: The catalytic domain of human immunodeficiency virus integrase: ordered active site in the F185H mutant. Authors: Bujacz, G. / Alexandratos, J. / Qing, Z.L. / Clement-Mella, C. / Wlodawer, A. #1: ![]() Title: High-Resolution Structure of the Catalytic Domain of Avian Sarcoma Virus Integrase Authors: Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Katz, R.A. / Skalka, A.M. #2: ![]() 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 | ![]() | 45.6 KB | Display | ![]() |
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PDB format | ![]() | 31.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.5 KB | Display | ![]() |
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Full document | ![]() | 392.2 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1itgS S: Starting model for refinement |
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Similar structure data |
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Links
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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 / Fragment: CATALYTIC CORE DOMAIN 50 - 212 / Mutation: F185H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: EXPRESSION CLONE FOR CORE, REFER TO PNAS USA, VOL. 90, PP3428-3432, APRIL 1993, AND PNAS USA, VOL. 92, PP.6057-6061, JUNE 1995 Cell line: BL21 / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 3-9% PEG 8000, 0.4M AMMONIUM SULFATE, 0.1M SODIUM CACODYLATE PH 6.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||
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: RIGAKU / Detector: IMAGE PLATE / Date: Apr 5, 1996 / Details: DOUBLE FOCUSSING MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→10 Å / Num. obs: 5012 / % possible obs: 79.8 % / Observed criterion σ(I): 0 / Redundancy: 2.93 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.63 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 1.38 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 1.88 / % possible all: 54.4 |
Reflection | *PLUS Num. measured all: 14682 |
Reflection shell | *PLUS % possible obs: 54.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ITG Resolution: 2.6→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 34.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |