+Open data
-Basic information
Entry | Database: PDB / ID: 8j1g | ||||||
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Title | Structure of amino acid dehydrogenase in complex with NADPH | ||||||
Components | Ornithine cyclodeaminase family protein | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Pseudomonas veronii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sakuraba, H. / Ohshima, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j1g.cif.gz | 483.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j1g.ent.gz | 400.8 KB | Display | PDB format |
PDBx/mmJSON format | 8j1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j1g_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8j1g_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8j1g_validation.xml.gz | 46.6 KB | Display | |
Data in CIF | 8j1g_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/8j1g ftp://data.pdbj.org/pub/pdb/validation_reports/j1/8j1g | HTTPS FTP |
-Related structure data
Related structure data | 8j1cC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Pseudomonas veronii (bacteria) / Gene: HBO43_18005 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Y0ZV07 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 38.301 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R: 0.452 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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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