[English] 日本語
Yorodumi- PDB-2ygk: Crystal structure of the NurA nuclease from Sulfolobus solfataricus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ygk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the NurA nuclease from Sulfolobus solfataricus | ||||||
Components | NURA | ||||||
Keywords | HYDROLASE / DNA REPAIR / REPLICATION | ||||||
Function / homology | NurA domain / NurA domain / NurA / nuclease activity / Hydrolases; Acting on ester bonds / DNA repair / metal ion binding / : / DNA double-strand break repair nuclease NurA Function and homology information | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Rzechorzek, N.J. / Blackwood, J.K. / Abrams, A.S. / Maman, J.D. / Robinson, N.P. / Pellegrini, L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Structural and Functional Insights Into DNA-End Processing by the Archaeal Hera Helicase-Nura Nuclease Complex. Authors: Blackwood, J.K. / Rzechorzek, N.J. / Abrams, A.S. / Maman, J.D. / Pellegrini, L. / Robinson, N.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ygk.cif.gz | 270.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ygk.ent.gz | 229.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ygk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ygk_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ygk_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 2ygk_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 2ygk_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2ygk ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2ygk | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.2952, 0.9554), Vector: |
-Components
#1: Protein | Mass: 39649.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)ROSETTA / References: UniProt: Q97WH1 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.7 % / Description: NONE |
---|---|
Crystal grow | pH: 4.5 Details: 0.1 M SODIUM CITRATE PH 4.5, 1 M LITHIUM CHLORIDE, 5% W/V PEG 6K, 50 MM MANGANESE CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→35.94 Å / Num. obs: 24087 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.5→35.94 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 28.798 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.01 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→35.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|