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Yorodumi- PDB-7yb1: Crystal Structure of anthrol reductase (CbAR) in complex with NADP+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yb1 | |||||||||||||||
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Title | Crystal Structure of anthrol reductase (CbAR) in complex with NADP+ | |||||||||||||||
Components | Versicolorin reductase | |||||||||||||||
Keywords | OXIDOREDUCTASE / anthrol reductase / chiral alcohol / emodin | |||||||||||||||
Function / homology | Function and homology information organic substance biosynthetic process / cellular biosynthetic process / oxidoreductase activity, acting on CH-OH group of donors Similarity search - Function | |||||||||||||||
Biological species | Cercospora sp. JNU001 (fungus) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||||||||
Authors | Hou, X.D. / Rao, Y.J. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural analysis of an anthrol reductase inspires enantioselective synthesis of enantiopure hydroxycycloketones and beta-halohydrins. Authors: Hou, X. / Xu, H. / Yuan, Z. / Deng, Z. / Fu, K. / Gao, Y. / Liu, C. / Zhang, Y. / Rao, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yb1.cif.gz | 198.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yb1.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 7yb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/7yb1 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/7yb1 | HTTPS FTP |
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-Related structure data
Related structure data | 7yb2C 8hfjC 8hfkC 3is3S 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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Unit cell |
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-Components
#1: Protein | Mass: 30115.912 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cercospora sp. JNU001 (fungus) / Gene: CB0940_02504 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G5I2X5 #2: Chemical | ChemComp-NAP / #3: 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: 2.18 Å3/Da / Density % sol: 43.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 7.5, 15% isopropanol and 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Sep 22, 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→23.66 Å / Num. obs: 15527 / % possible obs: 99.17 % / Redundancy: 5.13 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.2 | ||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IS3 Resolution: 3.3→23.66 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.791 / SU B: 37.879 / SU ML: 0.606 / Cross valid method: THROUGHOUT / ESU R Free: 0.678 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.774 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→23.66 Å
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Refine LS restraints |
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