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Open data
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Basic information
Entry | Database: PDB / ID: 4q16 | ||||||
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Title | Structure of NAD+ Synthetase from Deinococcus radiodurans | ||||||
![]() | NH(3)-dependent NAD(+) synthetase | ||||||
![]() | LIGASE / NADS / NAD synthetase | ||||||
Function / homology | ![]() NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, J.Y. / Park, Y.W. | ||||||
![]() | ![]() Title: Structural Analysis of the NH3-dependent NAD+ Synthetase from Deinococcus radiodurans Authors: Lee, J.Y. / Park, Y.W. / Yeo, H.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.5 KB | Display | ![]() |
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PDB format | ![]() | 170.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.9 KB | Display | ![]() |
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Full document | ![]() | 474.6 KB | Display | |
Data in XML | ![]() | 40.9 KB | Display | |
Data in CIF | ![]() | 57.2 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31112.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: R1 / Gene: nadE, DR_A0201 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.05 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: 20% Poly ethylene glycol (PEG) 4000, 0.2M lithium sulfate, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2013 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 49185 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 37.09 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.44 Å2 / Biso mean: 41.74 Å2 / Biso min: 14.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.381 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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