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Yorodumi- PDB-1sh9: Comparing the Accumulation of Active Site and Non-active Site Mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sh9 | ||||||
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Title | Comparing the Accumulation of Active Site and Non-active Site Mutations in the HIV-1 Protease | ||||||
Components | POL polyprotein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / non-active site mutations / active site mutations / ritonavir / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Clemente, J.C. / Moose, R.E. / Hemrajani, R. / Govindasamy, L. / Reutzel, R. / McKenna, R. / Abanje-McKenna, M. / Goodenow, M.M. / Dunn, B.M. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Comparing the Accumulation of Active- and Nonactive-Site Mutations in the HIV-1 Protease. Authors: Clemente, J.C. / Moose, R.E. / Hemrajani, R. / Whitford, L.R. / Govindasamy, L. / Reutzel, R. / McKenna, R. / Agbandje-McKenna, M. / Goodenow, M.M. / Dunn, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sh9.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sh9.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 1sh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/1sh9 ftp://data.pdbj.org/pub/pdb/validation_reports/sh/1sh9 | HTTPS FTP |
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-Related structure data
Related structure data | 1sguC 1hxwS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 10835.717 Da / Num. of mol.: 2 / Fragment: PROTEASE Mutation: K20R, V32I, L33F, M36I, I54V, L63P, A71V, V82A, I84V, L90M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-RIT / | #3: 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: 2.09 Å3/Da / Density % sol: 40.61 % |
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Crystal grow | Temperature: 298 K / pH: 6 Details: 20mM Sodium Acetate, 1.5 M Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→19.77 Å / Num. obs: 6598 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.134 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.48→2.59 Å / Rsym value: 0.511 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HXW Resolution: 2.5→19.77 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 216954.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.96 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
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Xplor file |
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