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Open data
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Basic information
Entry | Database: PDB / ID: 1biu | ||||||
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Title | HIV-1 INTEGRASE CORE DOMAIN COMPLEXED WITH MG++ | ||||||
![]() | HIV-1 INTEGRASE | ||||||
![]() | DNA INTEGRATION / INTEGRASE / HIV / HYDROLASE / ASPARTYL PROTEASE / ENDONUCLEASE | ||||||
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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Goldgur, Y. / Dyda, F. / Hickman, A.B. / Jenkins, T.M. / Craigie, R. / Davies, D.R. | ||||||
![]() | ![]() Title: Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium. Authors: Goldgur, Y. / Dyda, F. / Hickman, A.B. / Jenkins, T.M. / Craigie, R. / Davies, D.R. #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 | ![]() | 128.6 KB | Display | ![]() |
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PDB format | ![]() | 99.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.4 KB | Display | ![]() |
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Full document | ![]() | 385 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bisC ![]() 1bizC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 18123.639 Da / Num. of mol.: 3 / Fragment: CORE DOMAIN / Mutation: W131E, F185K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 4000, 100 MM HEPES, PH 7.0, 5 MM DTT, 5 MM MGCL2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.95 Å / Num. obs: 20883 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 8.6 / % possible all: 83.8 |
Reflection | *PLUS % possible obs: 96 % |
Reflection shell | *PLUS % possible obs: 75.6 % / Rmerge(I) obs: 0.083 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ITG Rfactor Rfree error: 0.009 / Highest resolution: 2.5 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.54 Å / Rfactor Rfree error: 0.072 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.41 |