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- PDB-2ygk: Crystal structure of the NurA nuclease from Sulfolobus solfataricus -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ygk | ||||||
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Title | Crystal structure of the NurA nuclease from Sulfolobus solfataricus | ||||||
![]() | NURA | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rzechorzek, N.J. / Blackwood, J.K. / Abrams, A.S. / Maman, J.D. / Robinson, N.P. / Pellegrini, L. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 270.4 KB | Display | ![]() |
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PDB format | ![]() | 229.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439 KB | Display | ![]() |
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Full document | ![]() | 447.8 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.2952, 0.9554), Vector: |
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Components
#1: Protein | Mass: 39649.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.7 % / Description: NONE |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 2.5→35.94 Å
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Refine LS restraints |
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