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Yorodumi- PDB-7cyi: Crystal structure of Alcohol dehydrogenase 1 from Artemisia annua -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cyi | ||||||||||||
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Title | Crystal structure of Alcohol dehydrogenase 1 from Artemisia annua | ||||||||||||
Components | Alcohol dehydrogenase 1 | ||||||||||||
Keywords | OXIDOREDUCTASE / Sesquiterpene biosynthesis / dehydrogenase / zinc ion binding | ||||||||||||
Function / homology | Function and homology information : / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Artemisia annua (sweet wormwood) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||||||||
Authors | Feng, X. / Fan, S. / Lv, G. / Li, M. / Wu, G. / Jin, Y. / Yang, Z. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Crystal structure of Alcohol dehydrogenase 1 from Artemisia annua Authors: Yang, Z. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cyi.cif.gz | 280.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cyi.ent.gz | 225.9 KB | Display | PDB format |
PDBx/mmJSON format | 7cyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cyi_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 7cyi_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 7cyi_validation.xml.gz | 50 KB | Display | |
Data in CIF | 7cyi_validation.cif.gz | 68 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/7cyi ftp://data.pdbj.org/pub/pdb/validation_reports/cy/7cyi | HTTPS FTP |
-Related structure data
Related structure data | 6ljhS S: Starting model for refinement |
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Similar structure data |
-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: 41532.996 Da / Num. of mol.: 4 / Mutation: L19S, G20S, V78I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Artemisia annua (sweet wormwood) / Gene: ADH1, CTI12_AA090660 / Production host: Escherichia coli (E. coli) References: UniProt: A0A2U1Q018, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-ZN / #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: 3.15 Å3/Da / Density % sol: 60.94 % |
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Crystal grow | Temperature: 289.15 K / Method: evaporation / Details: PEG 8000, Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→50 Å / Num. obs: 41150 / % possible obs: 97 % / Redundancy: 3.4 % / Biso Wilson estimate: 53.45 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.075 / Rrim(I) all: 0.14 / Χ2: 0.959 / Net I/σ(I): 5.8 / Num. measured all: 138337 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LJH Resolution: 2.95→38.96 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0.36 / Phase error: 30.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.51 Å2 / Biso mean: 46.0539 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.95→38.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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