+Open data
-Basic information
Entry | Database: PDB / ID: 1bis | ||||||
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Title | HIV-1 INTEGRASE CORE DOMAIN | ||||||
Components | HIV-1 INTEGRASE | ||||||
Keywords | DNA INTEGRATION / INTEGRASE / HIV / HYDROLASE / ASPARTYL PROTEASE / ENDONUCLEASE | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Goldgur, Y. / Dyda, F. / Hickman, A.B. / Jenkins, T.M. / Craigie, R. / Davies, D.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 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: 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 | 1bis.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bis.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bis_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 1bis_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 1bis_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1bis_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/1bis ftp://data.pdbj.org/pub/pdb/validation_reports/bi/1bis | HTTPS FTP |
-Related structure data
Related structure data | 1biuC 1bizC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.456182, -0.889688, 0.018811), Vector: |
-Components
#1: Protein | Mass: 18134.643 Da / Num. of mol.: 2 / Fragment: CORE DOMAIN / Mutation: W131E, F185K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P12497 #2: 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: 2.18 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 shell | *PLUS % possible obs: 83.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ITG Rfactor Rfree error: 0.008 / Highest resolution: 1.95 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: 1.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→1.98 Å / Rfactor Rfree error: 0.068 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.361 |