+Open data
-Basic information
Entry | Database: PDB / ID: 1hpz | ||||||
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Title | HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 | ||||||
Components | (POL POLYPROTEIN) x 2 | ||||||
Keywords | TRANSFERASE / NUCLEOTIDYLTRANSFERASE | ||||||
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ding, J. / Hsiou, Y. / Arnold, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance. Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Jr., A.D. / Boyer, P.L. / Lewi, P. / Janssen, P.A. / Kleim, J.P. / Rosner, M. / Hughes, S.H. / Arnold, E. #1: Journal: Structure / Year: 1995 Title: Structure of HIV-1 Reverse Transcriptase in a Complex with the Nonnucleoside Inhibitor Alpha-APA R95845 at 2.8 A Resolution Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Jr., A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hpz.cif.gz | 205.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hpz.ent.gz | 161.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/1hpz ftp://data.pdbj.org/pub/pdb/validation_reports/hp/1hpz | HTTPS FTP |
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-Related structure data
Related structure data | 1hqeC 1hquC 1hniS 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: 64485.887 Da / Num. of mol.: 1 / Fragment: P66 SUBUNIT / Mutation: K103N, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: HIV-1 CLONE 12; / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 ISOLATE / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 50266.684 Da / Num. of mol.: 1 / Fragment: P51 SUBUNIT / Mutation: K103N, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: HIV-1 CLONE 12 / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 ISOLATE / References: UniProt: P03366, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-AAP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Bis-Tris.propane, ammoniun sulfate, glycerol, PEG 8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 195243 / Num. obs: 29927 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 5 % / Rmerge(I) obs: 0.38 / % possible all: 93.7 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 195243 |
Reflection shell | *PLUS % possible obs: 94.2 % / Rmerge(I) obs: 0.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HNI Resolution: 3→25 Å / σ(F): 2 / Stereochemistry target values: Engh and Huber
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Displacement parameters | Biso mean: 65.4 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→25 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 25 Å / σ(F): 2 / % reflection Rfree: 4.56 % / Rfactor obs: 0.259 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 65.4 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å / Rfactor Rfree: 0.356 / Rfactor obs: 0.345 |