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Yorodumi- PDB-1a43: STRUCTURE OF THE HIV-1 CAPSID PROTEIN DIMERIZATION DOMAIN AT 2.6A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a43 | ||||||
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Title | STRUCTURE OF THE HIV-1 CAPSID PROTEIN DIMERIZATION DOMAIN AT 2.6A RESOLUTION | ||||||
Components | HIV-1 CAPSID | ||||||
Keywords | VIRAL PROTEIN / CAPSID / ASSEMBLY PROTEIN / HIV-1 | ||||||
Function / homology | Function and homology information 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Worthylake, D.K. / Wang, H. / Yoo, S. / Sundquist, W.I. / Hill, C.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structures of the HIV-1 capsid protein dimerization domain at 2.6 A resolution. Authors: Worthylake, D.K. / Wang, H. / Yoo, S. / Sundquist, W.I. / Hill, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a43.cif.gz | 22.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a43.ent.gz | 16.5 KB | Display | PDB format |
PDBx/mmJSON format | 1a43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a43_validation.pdf.gz | 420.7 KB | Display | wwPDB validaton report |
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Full document | 1a43_full_validation.pdf.gz | 421.6 KB | Display | |
Data in XML | 1a43_validation.xml.gz | 5 KB | Display | |
Data in CIF | 1a43_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a43 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a43 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9662.116 Da / Num. of mol.: 1 Fragment: C-TERMINAL DOMAIN OF HIV-1 CAPSID PROTEIN RESIDUES 146-231 (CAPSID NUMBERING) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12497 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.86 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: drop contained 1:1 mixture of protein and reservoir solution | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 3102 / Observed criterion σ(I): 0 / Biso Wilson estimate: 59.6 Å2 |
Reflection | *PLUS Num. obs: 3166 / % possible obs: 91.3 % / Num. measured all: 21325 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 92.5 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 5.9 |
-Processing
Software |
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Refinement | Resolution: 2.6→20 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 71 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.069 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.377 |