[English] 日本語
Yorodumi- PDB-7w5n: The crystal structure of the reduced form of Gluconobacter oxydan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w5n | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of the reduced form of Gluconobacter oxydans WSH-004 SNDH | ||||||
Components | L-sorbosone dehydrogenase, NAD(P) dependent | ||||||
Keywords | OXIDOREDUCTASE / L-sorbosone dehydrogenase / NAD(P)+ | ||||||
Function / homology | Chem-NDP Function and homology information | ||||||
Biological species | Gluconobacter oxydans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.988 Å | ||||||
Authors | Li, D. / Hou, X.D. / Rao, Y.J. / Yin, D.J. / Zhou, J.W. / Chen, J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Adv Sci / Year: 2023 Title: Structural Insight into the Catalytic Mechanisms of an L-Sorbosone Dehydrogenase. Authors: Li, D. / Deng, Z. / Hou, X. / Qin, Z. / Wang, X. / Yin, D. / Chen, Y. / Rao, Y. / Chen, J. / Zhou, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7w5n.cif.gz | 366.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7w5n.ent.gz | 300.3 KB | Display | PDB format |
PDBx/mmJSON format | 7w5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/7w5n ftp://data.pdbj.org/pub/pdb/validation_reports/w5/7w5n | HTTPS FTP |
---|
-Related structure data
Related structure data | 7w5kC 7w5lC 3u4jS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 54454.000 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Strain: WSH-004 / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-NDP / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.36 % |
---|---|
Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, sitting drop / Details: succinic acid, hepes, pegme 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Jul 29, 2020 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.988→23.516 Å / Num. obs: 41320 / % possible obs: 99.18 % / Redundancy: 8.86 % / Biso Wilson estimate: 22.89 Å2 / Rsym value: 0.313 / Net I/av σ(I): 15.294 / Net I/σ(I): 9.88 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U4J Resolution: 2.988→23.516 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.875 / SU B: 16.877 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 17.85 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.988→23.516 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|