+Open data
-Basic information
Entry | Database: PDB / ID: 5ght | ||||||
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Title | DNA replication protein | ||||||
Components | SsDNA-specific exonuclease | ||||||
Keywords | DNA BINDING PROTEIN / DNA replication | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 Å | ||||||
Authors | Oyama, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. Authors: Oyama, T. / Ishino, S. / Shirai, T. / Yamagami, T. / Nagata, M. / Ogino, H. / Kusunoki, M. / Ishino, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ght.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ght.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ght.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ght_validation.pdf.gz | 430.7 KB | Display | wwPDB validaton report |
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Full document | 5ght_full_validation.pdf.gz | 434.4 KB | Display | |
Data in XML | 5ght_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 5ght_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/5ght ftp://data.pdbj.org/pub/pdb/validation_reports/gh/5ght | HTTPS FTP |
-Related structure data
Related structure data | 5ghrSC 5ghsC 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: 52910.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1252 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5JGL0 |
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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: 3.11 Å3/Da / Density % sol: 60.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.795→50 Å / Num. obs: 16452 / % possible obs: 99.9 % / Redundancy: 13.7 % / Net I/σ(I): 45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GHR Resolution: 2.795→42.263 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.795→42.263 Å
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Refine LS restraints |
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LS refinement shell |
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