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- PDB-1nqz: The structure of a CoA pyrophosphatase from D. Radiodurans comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nqz | ||||||
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Title | The structure of a CoA pyrophosphatase from D. Radiodurans complexed with a magnesium ion | ||||||
![]() | CoA pyrophosphatase (MutT/nudix family protein) | ||||||
![]() | HYDROLASE / Nudix / MutT / pyrophosphatase / CoA / D.Radiodurans | ||||||
Function / homology | ![]() coenzyme A diphosphatase activity / coenzyme A catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kang, L.W. / Gabelli, S.B. / Bianchet, M.A. / Xu, W.L. / Bessman, M.J. / Amzel, L.M. | ||||||
![]() | ![]() Title: Structure of a coenzyme A pyrophosphatase from Deinococcus radiodurans: a member of the Nudix family. Authors: Kang, L.W. / Gabelli, S.B. / Bianchet, M.A. / Xu, W.L. / Bessman, M.J. / Amzel, L.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 | ![]() | 48.7 KB | Display | ![]() |
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PDB format | ![]() | 33.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370.7 KB | Display | ![]() |
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Full document | ![]() | 373.5 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nqySC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 21273.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dr1184 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.21 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG1500, MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 19112 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.062 / Net I/σ(I): 15.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 100105 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 97.5 % / Mean I/σ(I) obs: 5.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NQY Resolution: 1.7→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.325 / Rfactor Rwork: 0.313 |