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Open data
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Basic information
Entry | Database: PDB / ID: 6a3f | ||||||
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Title | Levoglucosan dehydrogenase, apo form | ||||||
![]() | 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 | ![]() | 168.5 KB | Display | ![]() |
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PDB format | ![]() | 130.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451 KB | Display | ![]() |
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Full document | ![]() | 454.5 KB | Display | |
Data in XML | ![]() | 32.2 KB | Display | |
Data in CIF | ![]() | 47.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a3gC ![]() 6a3iC ![]() 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 on special symmetry positions |
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Components
#1: Protein | Mass: 44334.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 18606 / JCM 16027 / LMG 23796 / Sphe3 / Gene: Asphe3_10730 / Plasmid: pET28a / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: sodium cacodylate, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 28, 2015 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 74076 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 35.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3610 / CC1/2: 0.974 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4H3V Resolution: 1.8→38.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.636 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.111 / 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: 27.844 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→38.28 Å
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Refine LS restraints |
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