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Open data
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Basic information
Entry | Database: PDB / ID: 8j1c | ||||||
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Title | Structure of amino acid dehydrogenase in complex with NADP | ||||||
![]() | 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 / IMIDAZOLE / LYSINE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 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 | ![]() | 244.5 KB | Display | ![]() |
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PDB format | ![]() | 195.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8j1gC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36036.043 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 241 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-LYS / | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 8000, imidazole buffer, NaCl, NADP, lysine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 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: 2.2→46.8 Å / Num. obs: 70419 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Χ2: 0.97 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.2→2.25 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.192 / Num. measured all: 30922 / Num. unique obs: 4445 / CC1/2: 0.73 / Rpim(I) all: 0.487 / Rrim(I) all: 1.288 / Χ2: 0.98 / Net I/σ(I) obs: 1.7 |
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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: 48.631 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→46.8 Å
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Refine LS restraints |
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