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Yorodumi- PDB-4wyh: Crystal structure of PriX from the hyperthermophilic archaeon Sul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wyh | ||||||
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Title | Crystal structure of PriX from the hyperthermophilic archaeon Sulfolobus solfataricus | ||||||
Components | Uncharacterized protein | ||||||
Keywords | REPLICATION / A novel noncatalytic subunit archaeal eukaryal-type primase | ||||||
Function / homology | Primase X / Primase X / IODIDE ION / Primase X domain-containing protein Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.95 Å | ||||||
Authors | Ouyang, S. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase. Authors: Liu, B. / Ouyang, S. / Makarova, K.S. / Xia, Q. / Zhu, Y. / Li, Z. / Guo, L. / Koonin, E.V. / Liu, Z.J. / Huang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wyh.cif.gz | 35.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wyh.ent.gz | 23.4 KB | Display | PDB format |
PDBx/mmJSON format | 4wyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/4wyh ftp://data.pdbj.org/pub/pdb/validation_reports/wy/4wyh | HTTPS FTP |
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-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: 15130.359 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0502 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZS7 | ||
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#2: Chemical | ChemComp-IOD / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.28 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M potassium iodide, 20% (w/v) polyethylene glycol 3,350, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ELECTRON MICROSCOPE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→23.424 Å / Num. obs: 6218 / % possible obs: 92.81 % / Redundancy: 11.8 % / Net I/σ(I): 105.56 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→23.424 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.22 / 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: 1.95→23.424 Å
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Refine LS restraints |
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LS refinement shell |
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