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Open data
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Basic information
Entry | Database: PDB / ID: 8j1g | ||||||
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Title | Structure of amino acid dehydrogenase in complex with NADPH | ||||||
![]() | Ornithine cyclodeaminase family protein | ||||||
![]() | OXIDOREDUCTASE / dehydrogenase | ||||||
Function / homology | Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding domain superfamily / ARGININE / Chem-NDP / Ornithine cyclodeaminase family protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sakuraba, H. / Ohshima, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: First crystal structure of an NADP + -dependent l-arginine dehydrogenase belonging to the mu-crystallin family. Authors: Kawakami, R. / Takami, N. / Hayashi, J. / Yoneda, K. / Ohmori, T. / Ohshima, T. / Sakuraba, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 483.7 KB | Display | ![]() |
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PDB format | ![]() | 400.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 46.6 KB | Display | |
Data in CIF | ![]() | 61.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j1cC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 36036.043 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-ARG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: PEG 4000, Na acetate buffer, glycerol, NADPH, arginine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2022 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.8 Å / Num. obs: 56308 / % possible obs: 98.7 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Χ2: 0.99 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.5→2.57 Å / % possible obs: 98.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 1.2 / Num. measured all: 31137 / Num. unique obs: 4614 / CC1/2: 0.657 / Rpim(I) all: 0.495 / Rrim(I) all: 1.3 / Χ2: 0.96 / Net I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.876 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→47.8 Å
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Refine LS restraints |
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