+Open data
-Basic information
Entry | Database: PDB / ID: 7xwh | ||||||
---|---|---|---|---|---|---|---|
Title | structure of patulin-detoxifying enzyme with NADP+ | ||||||
Components | Short-chain dehydrogenase/reductase | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenases/reductase | ||||||
Function / homology | : / alcohol dehydrogenase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain dehydrogenase/reductase Function and homology information | ||||||
Biological species | Meyerozyma guilliermondii (fungus) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.31 Å | ||||||
Authors | Dai, L. / Li, H. / Hu, Y. / Guo, R.T. / Chen, C.C. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 Title: Structure-based rational design of a short-chain dehydrogenase/reductase for improving activity toward mycotoxin patulin. Authors: Dai, L. / Li, H. / Huang, J.W. / Hu, Y. / He, M. / Yang, Y. / Min, J. / Guo, R.T. / Chen, C.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xwh.cif.gz | 199.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xwh.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/7xwh ftp://data.pdbj.org/pub/pdb/validation_reports/xw/7xwh | HTTPS FTP |
---|
-Related structure data
Related structure data | 7xwiC 7xwjC 7xwkC 7xwlC 7xwmC 7xwnC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28070.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Meyerozyma guilliermondii (fungus) / Gene: SDR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A888VSF1, alcohol dehydrogenase #2: Chemical | ChemComp-NAP / #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: 2.1 Å3/Da / Density % sol: 41.4 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG Smear Broad, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Jun 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→35.6 Å / Num. obs: 41102 / % possible obs: 99.1 % / Redundancy: 2.84 % / Rmerge(I) obs: 0.0114 / Net I/σ(I): 5.78 |
Reflection shell | Resolution: 2.31→2.35 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 2024 / % possible all: 95.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.31→35.6 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.716 / SU ML: 0.23 / SU R Cruickshank DPI: 0.4398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 133.19 Å2 / Biso mean: 25.413 Å2 / Biso min: 6.72 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.31→35.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.31→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|