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- PDB-2yf4: Crystal structure of DR2231, the MazG-like protein from Deinococc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yf4 | |||||||||
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Title | Crystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, Apo structure | |||||||||
![]() | MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE | |||||||||
![]() | HYDROLASE / DIMERIC DUTPASE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Goncalves, A.M.D. / deSanctis, D. / McSweeney, S.M. | |||||||||
![]() | ![]() Title: Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans. Authors: Goncalves, A.M.D. / Desanctis, D. / Mcsweeney, S.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 518.6 KB | Display | ![]() |
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PDB format | ![]() | 445.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 513.3 KB | Display | ![]() |
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Full document | ![]() | 533.4 KB | Display | |
Data in XML | ![]() | 45.2 KB | Display | |
Data in CIF | ![]() | 64.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yeuSC ![]() 2yf3C ![]() 2yf9C ![]() 2yfcC ![]() 2yfdC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16708.691 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: R1 / Plasmid: PET151/D-TOPO / Production host: ![]() ![]() References: UniProt: Q9RS96, nucleoside-triphosphate diphosphatase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.47 % / Description: NONE |
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Crystal grow | Details: 0.01M MAGNESIUM CHLORIDE,0.05M SODIUM CACODYLATE, PH 6.0, 1M LITHIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2009 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 137940 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 20.78 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 7.1 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YEU Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.358 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 25.723 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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