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Open data
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Basic information
Entry | Database: PDB / ID: 6a3i | ||||||
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Title | Levoglucosan dehydrogenase, complex with NADH and levoglucosan | ||||||
![]() | Putative dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / NADH-dependent dehydrogenase / Rossmann Fold / Gfo/Idh/MocA family | ||||||
Function / homology | ![]() levoglucosan dehydrogenase / oxidoreductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugiura, M. / Yamada, C. / Arakawa, T. / Fushinobu, S. | ||||||
![]() | ![]() Title: Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase. Authors: Sugiura, M. / Nakahara, M. / Yamada, C. / Arakawa, T. / Kitaoka, M. / Fushinobu, S. #1: Journal: Biosci. Biotechnol. Biochem. / Year: 1994 Title: Levoglucosan dehydrogenase involved in the assimilation of levoglucosan in Arthrobacter sp. I-552. Authors: Nakahara, K. / Kitamura, Y. / Yamagishi, Y. / Shoun, H. / Yasui, 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 | ![]() | 294.5 KB | Display | ![]() |
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PDB format | ![]() | 236.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 54.8 KB | Display | |
Data in CIF | ![]() | 73.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a3fC ![]() 6a3gC ![]() 6a3jC ![]() 4h3vS S: Starting model for refinement C: citing same article ( |
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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: 44334.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 18606 / JCM 16027 / LMG 23796 / Sphe3 / Gene: Asphe3_10730 / Plasmid: pET-28a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES-NaOH, PEG 3000, PEG 200, NADH, levoglucosan |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 5, 2016 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 51934 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2590 / CC1/2: 0.959 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4H3V Resolution: 2.41→34.84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.636 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 0.998 / ESU R Free: 0.354 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.786 Å2
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Refinement step | Cycle: 1 / Resolution: 2.41→34.84 Å
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Refine LS restraints |
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