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Yorodumi- PDB-7xwk: structure of patulin-detoxifying enzyme Y155F with NADPH and substrate -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xwk | ||||||
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Title | structure of patulin-detoxifying enzyme Y155F with NADPH and substrate | ||||||
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 / Chem-I8L / Chem-NDP / Short-chain dehydrogenase/reductase Function and homology information | ||||||
Biological species | Meyerozyma guilliermondii (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Dai, L. / Li, H. / Hu, Y. / Guo, R.T. / Chen, C.C. | ||||||
Funding support | 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xwk.cif.gz | 201.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xwk.ent.gz | 160.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xwk_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 7xwk_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 7xwk_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 7xwk_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/7xwk ftp://data.pdbj.org/pub/pdb/validation_reports/xw/7xwk | HTTPS FTP |
-Related structure data
Related structure data | 7xwhC 7xwiSC 7xwjC 7xwlC 7xwmC 7xwnC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27357.078 Da / Num. of mol.: 4 / Mutation: Y155F 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-NDP / #3: Chemical | ChemComp-I8L / ( #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.17 Å3/Da / Density % sol: 43.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 22-23% PEG Smear Broad, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 15, 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: 2.12→35.28 Å / Num. obs: 53451 / % possible obs: 99.9 % / Redundancy: 6.58 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 0.4457 |
Reflection shell | Resolution: 2.12→2.15 Å / Rmerge(I) obs: 0.4457 / Num. unique obs: 2199 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XWI Resolution: 2.12→35.28 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.438 / SU ML: 0.19 / SU R Cruickshank DPI: 0.2724 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 104.95 Å2 / Biso mean: 22.959 Å2 / Biso min: 6.15 Å2
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Refinement step | Cycle: final / Resolution: 2.12→35.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.175 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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