+Open data
-Basic information
Entry | Database: PDB / ID: 6a3j | ||||||
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Title | Levoglucosan dehydrogenase, complex with NADH and L-sorbose | ||||||
Components | Putative dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NADH-dependent dehydrogenase / Rossmann Fold / Gfo/Idh/MocA family | ||||||
Function / homology | Function and homology information levoglucosan dehydrogenase / oxidoreductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudarthrobacter phenanthrenivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sugiura, M. / Yamada, C. / Arakawa, T. / Fushinobu, S. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a3j.cif.gz | 314 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a3j.ent.gz | 251.3 KB | Display | PDB format |
PDBx/mmJSON format | 6a3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a3j_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 6a3j_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 6a3j_validation.xml.gz | 61.2 KB | Display | |
Data in CIF | 6a3j_validation.cif.gz | 87.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/6a3j ftp://data.pdbj.org/pub/pdb/validation_reports/a3/6a3j | HTTPS FTP |
-Related structure data
Related structure data | 6a3fC 6a3gC 6a3iC 4h3vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Pseudarthrobacter phenanthrenivorans (strain DSM 18606 / JCM 16027 / LMG 23796 / Sphe3) (bacteria) Strain: DSM 18606 / JCM 16027 / LMG 23796 / Sphe3 / Gene: Asphe3_10730 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: F0M433 #2: Chemical | #3: Sugar | ChemComp-SOE / #4: Chemical | ChemComp-NAI / #5: Water | ChemComp-HOH / | |
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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: 2.01 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES-NaOH, PEG3000, PEG 200, NADH, L-sorbose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 15, 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: 1.9→50 Å / Num. obs: 114792 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5696 / CC1/2: 0.936 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H3V Resolution: 1.9→49.49 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.191 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.135 / 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: 28.603 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→49.49 Å
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Refine LS restraints |
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