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Yorodumi- PDB-7eus: Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eus | |||||||||||||||
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Title | Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) from Cercospora sp. JNU001 | |||||||||||||||
Components | 2-oxoglutarate (2-OG)-dependent dioxygenase | |||||||||||||||
Keywords | OXIDOREDUCTASE / 2-oxoglutarate-dependent dioxygenase / cercosporin | |||||||||||||||
Function / homology | COPPER (II) ION Function and homology information | |||||||||||||||
Biological species | Cercospora sojina (fungus) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | |||||||||||||||
Authors | Hou, X.D. / Liu, X.Z. / Yuan, Z.B. / Rao, Y.J. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Molecular Basis of the Unusual Seven-Membered Methylenedioxy Bridge Formation Catalyzed by Fe(II)/alpha-KG-Dependent Oxygenase CTB9 Authors: Liu, X.Z. / Yuan, Z.B. / Su, H. / Hou, X.D. / Deng, Z.W. / Xu, H.B. / Guo, B.D. / Yin, D. / Sheng, X. / Rao, Y.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eus.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eus.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 7eus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/7eus ftp://data.pdbj.org/pub/pdb/validation_reports/eu/7eus | HTTPS FTP |
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-Related structure data
Related structure data | 7eutC 7euuC 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: 39008.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cercospora sojina (fungus) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 2.18 Å3/Da / Density % sol: 43.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 mM Bis-Tris pH 6.5, 3% (v/v) glycerol, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.29→50 Å / Num. obs: 28264 / % possible obs: 98.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.051 / Rrim(I) all: 0.135 / Χ2: 0.878 / Net I/σ(I): 6.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→42.62 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.798 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.233 / 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: 80.7 Å2 / Biso mean: 28.651 Å2 / Biso min: 12.93 Å2
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Refinement step | Cycle: final / Resolution: 2.3→42.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.291→2.351 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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