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Yorodumi- PDB-4ya6: Crystal structure of LigO-apo form from Sphingobium sp. strain SYK-6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ya6 | ||||||
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Title | Crystal structure of LigO-apo form from Sphingobium sp. strain SYK-6 | ||||||
Components | C alpha-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Short Chain Dehydrogenase/reductase SDR family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sphingobium sp. SYK-6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.799 Å | ||||||
Authors | Pereira, J.H. / McAndrew, R.P. / Heins, R.A. / Sale, K.L. / Simmons, B.A. / Adams, P.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. Authors: Pereira, J.H. / Heins, R.A. / Gall, D.L. / McAndrew, R.P. / Deng, K. / Holland, K.C. / Donohue, T.J. / Noguera, D.R. / Simmons, B.A. / Sale, K.L. / Ralph, J. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ya6.cif.gz | 164.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ya6.ent.gz | 132.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ya6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ya6_validation.pdf.gz | 418.5 KB | Display | wwPDB validaton report |
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Full document | 4ya6_full_validation.pdf.gz | 419.8 KB | Display | |
Data in XML | 4ya6_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4ya6_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/4ya6 ftp://data.pdbj.org/pub/pdb/validation_reports/ya/4ya6 | HTTPS FTP |
-Related structure data
Related structure data | 4y98C 4y9dC 4yacC 4yaeC 4yagC 4yaiC 4yapC 4yavC 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
#1: Protein | Mass: 32761.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligO, SLG_35880 / Production host: Escherichia coli (E. coli) / References: UniProt: C0SUK3 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Ammonium Citrate, 0.1 M MES pH 5.5, 20% PEG 3,350, 5% Isopropanol PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 24752 / % possible obs: 100 % / Redundancy: 10.8 % / Net I/σ(I): 46.3 |
-Processing
Software |
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Refinement | Resolution: 1.799→50 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.9 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.799→50 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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