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Yorodumi- PDB-6lql: Complex structure of CHAO with product from Erythrobacteraceae ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lql | ||||||
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Title | Complex structure of CHAO with product from Erythrobacteraceae bacterium | ||||||
Components | Amine oxidase | ||||||
Keywords | OXIDOREDUCTASE / Cyclohexylamine Oxidase | ||||||
Function / homology | Function and homology information Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Erythrobacteraceae bacterium CCH12-C2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Huang, Z.D. | ||||||
Citation | Journal: J.Org.Chem. / Year: 2020 Title: Asymmetric Synthesis of a Key Dextromethorphan Intermediate and Its Analogues Enabled by a New Cyclohexylamine Oxidase: Enzyme Discovery, Reaction Development, and Mechanistic Insight. Authors: Wu, X. / Huang, Z. / Wang, Z. / Li, Z. / Wang, J. / Lin, J. / Chen, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lql.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lql.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 6lql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lql_validation.pdf.gz | 1002.8 KB | Display | wwPDB validaton report |
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Full document | 6lql_full_validation.pdf.gz | 1008.8 KB | Display | |
Data in XML | 6lql_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 6lql_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/6lql ftp://data.pdbj.org/pub/pdb/validation_reports/lq/6lql | HTTPS FTP |
-Related structure data
Related structure data | 6lqcC 4i59S S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48990.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erythrobacteraceae bacterium CCH12-C2 (bacteria) Gene: CCH12-C2 / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-F0C / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Sequence details | WP_067401762.1 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0 % PEG 8000,100 mM Potassium phosphate monobasic/ Sodium phosphate dibasic pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2019 |
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: 58605 / % possible obs: 100 % / Redundancy: 25.9 % / Biso Wilson estimate: 24.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.028 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2866 / Rpim(I) all: 0.179 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I59 Resolution: 1.8→24.03 Å / SU ML: 0.1892 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.9225 / 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: 26.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→24.03 Å
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Refine LS restraints |
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LS refinement shell |
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