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Yorodumi- PDB-1lv1: Crystal Structure Analysis of the non-active site mutant of tethe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lv1 | ||||||
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Title | Crystal Structure Analysis of the non-active site mutant of tethered HIV-1 protease to 2.1A resolution | ||||||
Components | HIV-1 protease | ||||||
Keywords | HYDROLASE / beta-ribbon flap | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase 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 / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kumar, M. / Kannan, K.K. / Hosur, M.V. / Bhavesh, N.S. / Chatterjee, A. / Mittal, R. / Hosur, R.V. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2002 Title: Effects of remote mutation on the autolysis of HIV-1 PR: X-ray and NMR investigations. Authors: Kumar, M. / Kannan, K.K. / Hosur, M.V. / Bhavesh, N.S. / Chatterjee, A. / Mittal, R. / Hosur, R.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lv1.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lv1.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 1lv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lv1 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lv1 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 21902.760 Da / Num. of mol.: 1 / Mutation: C95M/C1095A Source method: isolated from a genetically manipulated source Details: Tethered dimer linked by GGSSG / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04585, HIV-1 retropepsin |
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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: 2.18 Å3/Da / Density % sol: 43.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 5% saturated ammonium sulfate, 200mM sodium phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200HB / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 2001 / Details: Totally reflecting MSC mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. all: 51200 / Num. obs: 11676 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.1→2.2 Å / % possible all: 47 |
Reflection | *PLUS Num. obs: 10245 / Num. measured all: 51200 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 85 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→14.75 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 319647.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.9922 Å2 / ksol: 0.326686 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→14.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.072 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 15 Å / Num. reflection obs: 7619 / Rfactor obs: 0.1935 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.1935 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.392 / Rfactor Rwork: 0.2924 / Rfactor obs: 0.2924 |