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Yorodumi- PDB-7ksf: Crystal structure of Prototype Foamy Virus Protease-Reverse Trans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ksf | |||||||||
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Title | Crystal structure of Prototype Foamy Virus Protease-Reverse Transcriptase (native) | |||||||||
Components | Protease/Reverse transcriptase/ribonuclease H | |||||||||
Keywords | VIRAL PROTEIN / Aspartyl protease / Hydrolase / Multifunctional enzyme / Transferase / reverse transcription / viral maturation | |||||||||
Function / homology | Function and homology information DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / proteolysis / RNA binding ...DNA integration / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / proteolysis / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Eastern chimpanzee simian foamy virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Harrison, J.J.E.K. / Das, K. / Ruiz, F.X. / Arnold, E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Viruses / Year: 2021 Title: Crystal Structure of a Retroviral Polyprotein: Prototype Foamy Virus Protease-Reverse Transcriptase (PR-RT). Authors: Harrison, J.J.E.K. / Tuske, S. / Das, K. / Ruiz, F.X. / Bauman, J.D. / Boyer, P.L. / DeStefano, J.J. / Hughes, S.H. / Arnold, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ksf.cif.gz | 195.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ksf.ent.gz | 123.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ksf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/7ksf ftp://data.pdbj.org/pub/pdb/validation_reports/ks/7ksf | HTTPS FTP |
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-Related structure data
Related structure data | 7kseSC S: Starting model for refinement C: citing same article (ref.) |
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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: 85173.031 Da / Num. of mol.: 1 / Mutation: D26A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern chimpanzee simian foamy virus / Gene: gag / Production host: Escherichia coli (E. coli) References: UniProt: A0A1Q1N9V8, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 50 mM KCl, 50 mM sodium cacodylate trihydrate pH 6.0, 12% PEG 8000, 1.0 mM spermine, 1.0 mM L-argininamide, 200 mM glycyglycine or glycylglycylglycine, 100 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.97601 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97601 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 19435 / % possible obs: 96.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 92.105 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.089 / Rrim(I) all: 0.157 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.532 / Mean I/σ(I) obs: 1 / Num. unique obs: 2867 / CC1/2: 0.334 / Rpim(I) all: 1.089 / Rrim(I) all: 1.888 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KSE Resolution: 2.9→50 Å / Cross valid method: FREE R-VALUE / σ(F): 43.83 / Phase error: 47.7899 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell |
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