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Yorodumi- PDB-6ljh: Crystal structure of Alcohol dehydrogenase 1 from Artemisia annua... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ljh | ||||||||||||
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Title | Crystal structure of Alcohol dehydrogenase 1 from Artemisia annua in complex with NAD+ | ||||||||||||
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: 1.8 Å | ||||||||||||
Authors | Feng, X. / Fan, S. / Li, M. / Zou, S. / Lv, G. / 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 in complex with NAD+ 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 | 6ljh.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ljh.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ljh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ljh_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 6ljh_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 6ljh_validation.xml.gz | 21 KB | Display | |
Data in CIF | 6ljh_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/6ljh ftp://data.pdbj.org/pub/pdb/validation_reports/lj/6ljh | HTTPS FTP |
-Related structure data
Related structure data | 4dl9S 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41532.996 Da / Num. of mol.: 1 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 |
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-Non-polymers , 5 types, 451 molecules
#2: Chemical | ChemComp-NAD / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MG256496 FOR THE PROTEIN. In MG256496, LEU(19th) ...AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MG256496 FOR THE PROTEIN. In MG256496, LEU(19th) is SEL, GLY(20th) is SEL and VAL(78th) is ILE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.85 % |
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Crystal grow | Temperature: 289.15 K / Method: evaporation / Details: PEG 10000, MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 41073 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Χ2: 0.928 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 4111 / CC1/2: 0.931 / Rpim(I) all: 0.174 / Rrim(I) all: 0.432 / Χ2: 1.002 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DL9 Resolution: 1.8→24.54 Å / SU ML: 0.1401 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.3676 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 23.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→24.54 Å
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Refine LS restraints |
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LS refinement shell |
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