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- PDB-7wwx: Crystal structure of Herbaspirillum huttiense L-arabinose 1-dehyd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wwx | ||||||
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Title | Crystal structure of Herbaspirillum huttiense L-arabinose 1-dehydrogenase (NAD bound form) | ||||||
![]() | NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) | ||||||
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Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matsubara, R. / Yoshiwara, K. / Watanabe, Y. / Watanabe, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of L-arabinose 1-dehydrogenase as a short-chain reductase/dehydrogenase protein. Authors: Watanabe, S. / Yoshiwara, K. / Matsubara, R. / Watanabe, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.7 KB | Display | ![]() |
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PDB format | ![]() | 94.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3nugS S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 29717.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DFS02_4196 / Production host: ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-PEG / | ![]() #4: 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: 2.29 Å3/Da / Density % sol: 46.34 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium formate, 20% PEG3350 |
-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: Oct 21, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.36→42.82 Å / Num. obs: 114656 / % possible obs: 99.8 % / Redundancy: 9.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.079 / Rrim(I) all: 0.249 / Net I/σ(I): 8.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3NUG Resolution: 1.36→42.82 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.979 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 51.82 Å2 / Biso mean: 12.04 Å2 / Biso min: 5.65 Å2
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Refinement step | Cycle: final / Resolution: 1.36→42.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.395 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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