+Open data
-Basic information
Entry | Database: PDB / ID: 3vrh | ||||||
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Title | Crystal structure of ph0300 | ||||||
Components | Putative uncharacterized protein PH0300 | ||||||
Keywords | RNA BINDING PROTEIN / ATPase / tRNA modification enzyme / thiolation | ||||||
Function / homology | Function and homology information Transferases; Transferring sulfur-containing groups; Sulfurtransferases / cytosolic tRNA wobble base thiouridylase complex / tRNA wobble position uridine thiolation / 4 iron, 4 sulfur cluster binding / transferase activity / tRNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Nakagawa, H. / Kuratani, M. / Goto-Ito, S. / Ito, T. / Sekine, S.I. / Yokoyama, S. | ||||||
Citation | Journal: Proteins / Year: 2013 Title: Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA. Authors: Nakagawa, H. / Kuratani, M. / Goto-Ito, S. / Ito, T. / Katsura, K. / Terada, T. / Shirouzu, M. / Sekine, S.I. / Shigi, N. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vrh.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vrh.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 3vrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vrh_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 3vrh_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 3vrh_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3vrh_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/3vrh ftp://data.pdbj.org/pub/pdb/validation_reports/vr/3vrh | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35691.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT-3 / Gene: PH0300 / Production host: Escherichia coli (E. coli) / References: UniProt: O58038 | ||||
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#2: Chemical | #3: Chemical | ChemComp-BCN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.39 % Description: The entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 12% PEG 3350, 0.2 M NaCl, 10% N,N-dimethylformamide, 0.1 M Bicine-NaOH, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 70 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 1, 2010 | |||||||||||||||||||||||||||||||||
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. all: 19954 / Num. obs: 19923 / % possible obs: 99.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 25.1 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→46.236 Å / SU ML: 0.31 / σ(F): 1.91 / Phase error: 24.03 / Stereochemistry target values: ML Details: The entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.677 Å2 / ksol: 0.333 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→46.236 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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