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Yorodumi- PDB-1f7a: HOW DOES A SYMMETRIC DIMER RECOGNIZE AN ASYMMETRIC SUBSTRATE? A S... -
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-Basic information
Entry | Database: PDB / ID: 1f7a | ||||||
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Title | HOW DOES A SYMMETRIC DIMER RECOGNIZE AN ASYMMETRIC SUBSTRATE? A SUBSTRATE COMPLEX OF HIV-1 PROTEASE. | ||||||
Components |
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Keywords | HYDROLASE / CAPSID / SUBSTRATE RECOGNITION | ||||||
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 / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Schiffer, C.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. Authors: Prabu-Jeyabalan, M. / Nalivaika, E. / 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 | 1f7a.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f7a.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 1f7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/1f7a ftp://data.pdbj.org/pub/pdb/validation_reports/f7/1f7a | HTTPS FTP |
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-Related structure data
Related structure data | 1mtrS 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: 10800.777 Da / Num. of mol.: 2 / Fragment: HIV-1 PROTEASE / Mutation: Q7K D25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03369, HIV-1 retropepsin #2: Protein/peptide | | Mass: 1077.298 Da / Num. of mol.: 1 / Fragment: CA-P2 SUBSTRATE / Source method: obtained synthetically / Details: This peptide was chemically synthesized. / References: UniProt: Q9YX54*PLUS #3: Chemical | ChemComp-ACT / #4: 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: 2.06 Å3/Da / Density % sol: 40.28 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 49525 / Num. obs: 12474 / % possible obs: 94.3 % / Redundancy: 5 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5 % / Rmerge(I) obs: 0.213 / Num. unique all: 738 / Rsym value: 21.3 / % possible all: 84 |
Reflection | *PLUS Num. measured all: 49525 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MTR Resolution: 2→26.37 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 304680.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.89 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→26.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.1 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.4 % / Rfactor obs: 0.197 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % reflection Rfree: 10.4 % |