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- PDB-2yf9: STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yf9 | |||||||||
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Title | STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, NATIVE FORM | |||||||||
![]() | MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE | |||||||||
![]() | HYDROLASE / DIMERIC DUTPASE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Goncalves, A.M.D. / De Sanctis, 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 | ![]() | 92.6 KB | Display | ![]() |
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PDB format | ![]() | 72.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.4 KB | Display | ![]() |
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Full document | ![]() | 414.2 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yeuSC ![]() 2yf3C ![]() 2yf4C ![]() 2yfcC ![]() 2yfdC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16708.691 Da / Num. of mol.: 1 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 | ||
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#2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 7 Details: 1.0 M LITHIUM CHLORIDE, 0.1 M CITRIC ACID, 5-10%(W/V) PEG 6000., pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2010 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97627 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.68 Å / Num. obs: 16383 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 23.21 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.2 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YEU Resolution: 1.899→45.683 Å / SU ML: 0.22 / σ(F): 1.37 / Phase error: 17.83 / 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 / Bsol: 56.991 Å2 / ksol: 0.359 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.899→45.683 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.4473 Å / Origin y: 13.7702 Å / Origin z: 12.1328 Å
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Refinement TLS group | Selection details: CHAIN A |