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Yorodumi- PDB-3pj6: Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pj6 | ||||||
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Title | Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants | ||||||
Components | HIV proteaseHIV-1 protease | ||||||
Keywords | HYDROLASE / Alternate conformations of Pro81 / proline switch / Wide-open flaps / Expanded active site cavity | ||||||
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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / 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 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Yedidi, R.S. / Proteasa, G. / Martinez-Cajas, J.L. / Vickrey, J.F. / Martin, P.D. / Wawrzak, Z. / Kovari, L.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Contribution of the 80s loop of HIV-1 protease to the multidrug-resistance mechanism: crystallographic study of MDR769 HIV-1 protease variants. Authors: Yedidi, R.S. / Proteasa, G. / Martinez, J.L. / Vickrey, J.F. / Martin, P.D. / Wawrzak, Z. / Liu, Z. / Kovari, I.A. / Kovari, L.C. | ||||||
History |
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Remark 999 | Author states that they are characteristic mutations of the original patient isolate MDR769 HIV-1 protease. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pj6.cif.gz | 32.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pj6.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 3pj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/3pj6 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/3pj6 | HTTPS FTP |
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-Related structure data
Related structure data | 3oq7C 3oqaC 3oqdC 1tw7S 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: 10725.582 Da / Num. of mol.: 1 / Fragment: UNP residues 1-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human Immunodeficiency Virus 1 / Strain: MDR769 / Gene: pol / Plasmid: pRSETB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysE / References: UniProt: Q000H7, UniProt: P35963*PLUS |
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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: 2.47 Å3/Da / Density % sol: 50.22 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.3-1.0 M NaCl, pH 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→27.66 Å / Num. all: 5356 / Num. obs: 5356 / Redundancy: 3.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.25→2.37 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY: 1TW7 Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.278 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.827 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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