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Yorodumi- PDB-7kse: Crystal structure of Prototype Foamy Virus Protease-Reverse Trans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kse | |||||||||
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Title | Crystal structure of Prototype Foamy Virus Protease-Reverse Transcriptase CSH mutant (selenomethionine-labeled) | |||||||||
Components | Peptidase A9/Reverse transcriptase/RNase 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 / SAD / Resolution: 3 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 | 7kse.cif.gz | 171.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kse.ent.gz | 127.4 KB | Display | PDB format |
PDBx/mmJSON format | 7kse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/7kse ftp://data.pdbj.org/pub/pdb/validation_reports/ks/7kse | HTTPS FTP |
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-Related 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: 85785.664 Da / Num. of mol.: 1 / Mutation: D26A, C282S, H509D, S586K 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: 2.88 Å3/Da / Density % sol: 57.22 % |
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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 |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3→50 Å / Num. obs: 19100 / % possible obs: 99.7 % / Redundancy: 30.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.331 / Rpim(I) all: 0.061 / Rrim(I) all: 0.337 / Net I/σ(I): 10.6 | |||||||||||||||
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 29.7 % / Rmerge(I) obs: 1.973 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2990 / CC1/2: 0.818 / Rpim(I) all: 0.367 / Rrim(I) all: 2.007 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→50 Å / Cross valid method: FREE R-VALUE / σ(F): 351.39 / Phase error: 37.4882 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: 86.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell |
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