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Yorodumi- PDB-4qj8: Crystal structure of inactive HIV-1 protease variant (I50V/A71V) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qj8 | ||||||
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Title | Crystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with p1-p6 substrate variant (P453L) | ||||||
Components |
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Keywords | HYDROLASE / co-evolution / protease | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...viral budding via host ESCRT complex / RNA stem-loop binding / host cell / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lin, K.H. / Schiffer, C.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease. Authors: Ozen, A. / Lin, K.H. / Kurt Yilmaz, N. / Schiffer, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qj8.cif.gz | 173 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qj8.ent.gz | 143.5 KB | Display | PDB format |
PDBx/mmJSON format | 4qj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/4qj8 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/4qj8 | HTTPS FTP |
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-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: 10828.831 Da / Num. of mol.: 4 / Mutation: Q7K, D25N, I50V, A71V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (ARV2/SF2 ISOLATE) Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap106 / References: UniProt: P03369, HIV-1 retropepsin #2: Protein/peptide | Mass: 1189.368 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Human immunodeficiency virus type 1 (ARV2/SF2 ISOLATE) References: UniProt: P03349*PLUS #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: 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 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: ammonium sulfate, sodium citrate, sodium phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2011 |
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→56.92 Å / Num. all: 61435 / Num. obs: 23065 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rsym value: 0.076 / Net I/σ(I): 13.51 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.69 / Rsym value: 0.214 / % possible all: 96.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→56.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.218 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2→56.92 Å
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