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Yorodumi- PDB-5vf4: Thermus aquaticus variable protein (TaqVP) from diversity-generat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vf4 | ||||||
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Title | Thermus aquaticus variable protein (TaqVP) from diversity-generating retroelements (DGR) | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / CLec-fold / Thermostable / DNA diversification | ||||||
Function / homology | Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / ACETATE ION / FGE-sulfatase domain-containing protein Function and homology information | ||||||
Biological species | Thermus aquaticus Y51MC23 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å | ||||||
Authors | Handa, S. / Ghosh, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: PLoS ONE / Year: 2019 Title: Crystal structure of a Thermus aquaticus diversity-generating retroelement variable protein. Authors: Handa, S. / Shaw, K.L. / Ghosh, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vf4.cif.gz | 576.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vf4.ent.gz | 495.9 KB | Display | PDB format |
PDBx/mmJSON format | 5vf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vf4_validation.pdf.gz | 480.9 KB | Display | wwPDB validaton report |
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Full document | 5vf4_full_validation.pdf.gz | 512.8 KB | Display | |
Data in XML | 5vf4_validation.xml.gz | 57.5 KB | Display | |
Data in CIF | 5vf4_validation.cif.gz | 79.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/5vf4 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/5vf4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 40977.934 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus Y51MC23 (bacteria) / Gene: TaqDRAFT_4799, TaqDRAFT_5434 / Production host: Escherichia coli (E. coli) / References: UniProt: B7A5T1 #2: Chemical | ChemComp-CA / #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: 4.32 Å3/Da / Density % sol: 71.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 15% (w/v) 2-methyl-2,4-pentanediol, 20 mm CaCl2, 100 mM Sodium Acetate (pH 4.6) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→134.27 Å / Num. obs: 132418 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.98 / Net I/σ(I): 12.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.81→80.814 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→80.814 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 55.5268 Å / Origin y: 74.5398 Å / Origin z: 74.1778 Å
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Refinement TLS group | Selection details: all |