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- PDB-3nug: Crystal structure of wild type tetrameric pyridoxal 4-dehydrogena... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nug | ||||||
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Title | Crystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti | ||||||
![]() | 3-oxoacyl-(Acyl-carrier protein) reductase | ||||||
![]() | OXIDOREDUCTASE / PYRIDOXAL / tPLDH / 4-PYRIDOXOLACTONE / SHORT CHAIN DEHYDROGENASE/REDUCTASE | ||||||
Function / homology | ![]() pyridoxal 4-dehydrogenase / pyridoxal 4-dehydrogenase activity / vitamin B6 catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chu, H.N. | ||||||
![]() | ![]() Title: The crystal structure of SDR-type pyridoxal 4-dehydrogenase of Mesorhizobium loti Authors: Chu, H.N. / Kobayashi, J. / Mikami, B. / Yagi, T. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Crystallization and preliminary X-ray analysis of SDR-type pyridoxal dehydrogenase from Mesorhizobium loti. Authors: Chu, H.N. / Kobayashi, J. / Yoshikane, Y. / Mikami, B. / Yagi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.4 KB | Display | ![]() |
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PDB format | ![]() | 170.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 46.9 KB | Display | |
Data in CIF | ![]() | 67.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ndrS S: Starting model for refinement |
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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
#1: Protein | Mass: 25426.914 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ACY / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.04 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Sodium acetate, 0.1M Tris-HCl, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 29, 2010 |
Radiation | Monochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.788→50 Å / Num. obs: 73944 / % possible obs: 96.5 % / Redundancy: 6.3 % / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.4 % / Num. unique all: 6986 / % possible all: 92.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NDR Resolution: 1.788→34.573 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.048 Å2 / ksol: 0.323 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.788→34.573 Å
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Refine LS restraints |
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LS refinement shell |
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