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Yorodumi- PDB-4obj: Crystal Structure of Inactive HIV-1 Protease in Complex with the ... -
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-Basic information
Entry | Database: PDB / ID: 4obj | ||||||
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Title | Crystal Structure of Inactive HIV-1 Protease in Complex with the p1-p6 substrate variant (S451N) | ||||||
Components |
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Keywords | HYDROLASE / Co-evolution / Resistance | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / 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 ...viral budding via host ESCRT complex / 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 / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Kolli, M. | ||||||
Citation | Journal: J.Virol. / Year: 2014 Title: HIV-1 protease-substrate coevolution in nelfinavir resistance. Authors: Kolli, M. / Ozen, A. / 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 | 4obj.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4obj.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 4obj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4obj_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 4obj_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 4obj_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4obj_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/4obj ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4obj | HTTPS FTP |
-Related structure data
Related structure data | 4obdC 4obfC 4obgC 4obhC 4obkC 1t3rS 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
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 10814.805 Da / Num. of mol.: 2 / Mutation: Q7K, D25N, V64I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: group M subtype B (isolate ARV2/SF2) / 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: 1200.350 Da / Num. of mol.: 1 / Fragment: UNP residues 446-455 / Mutation: S8N / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P03349 |
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-Non-polymers , 4 types, 172 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: 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: 38.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.0M Ammonium Sulphate, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.033 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 9, 2009 / Details: Mirrors |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 18954 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rsym value: 0.058 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 9.9 / Rsym value: 0.167 / % possible all: 96 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1T3R Resolution: 1.75→39.21 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.14 / SU ML: 0.061 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.105 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.845 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→39.21 Å
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Refine LS restraints |
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