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Yorodumi- PDB-1b9f: MOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WIT... -
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-Basic information
Entry | Database: PDB / ID: 1b9f | ||||||
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Title | MOBILITY OF AN HIV-1 INTEGRASE ACTIVE SITE LOOP IS CORRELATED WITH CATALYTIC ACTIVITY | ||||||
Components | PROTEIN (INTEGRASE) | ||||||
Keywords | TRANSFERASE / DNA INTEGRATION | ||||||
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 type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Greenwald, J. / Le, V. / Butler, S.L. / Bushman, F.D. / Choe, S. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity. Authors: Greenwald, J. / Le, V. / Butler, S.L. / Bushman, F.D. / Choe, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b9f.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b9f.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 1b9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b9f_validation.pdf.gz | 388 KB | Display | wwPDB validaton report |
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Full document | 1b9f_full_validation.pdf.gz | 393.9 KB | Display | |
Data in XML | 1b9f_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1b9f_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/1b9f ftp://data.pdbj.org/pub/pdb/validation_reports/b9/1b9f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17940.531 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN / Mutation: F185K, G140A, G149A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (CLONE 12) Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: 1 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P12497, RNA-directed DNA polymerase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Nonpolymer details | THE CAC RESIDUE IS A MODIFIED CACODYLATE WHERE THE SULFUR OF A CYS RESIDUE HAS REPLACED THE OH OF ...THE CAC RESIDUE IS A MODIFIED CACODYLATE | Sequence details | PDB SEQUENCE IS SINGLE DOMAIN OF POL_HV1N5 ENTRY. THERE ARE ALSO THREE POINT MUTATIONS OF F185K, G140A, G149A | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.45 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 22241 / % possible obs: 95.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.2 Å2 / Rsym value: 0.054 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 98.5 % / Rmerge(I) obs: 0.212 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / SU B: 2.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.12
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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