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Yorodumi- PDB-2oyk: Endo-glycoceramidase II from Rhodococcus sp.: cellobiose-like iso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oyk | |||||||||
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Title | Endo-glycoceramidase II from Rhodococcus sp.: cellobiose-like isofagomine complex | |||||||||
Components | Endoglycoceramidase II | |||||||||
Keywords | HYDROLASE / (alpha/beta)8 (TIM) barrel | |||||||||
Function / homology | Function and homology information endoglycosylceramidase / endoglycosylceramidase activity / carbohydrate derivative catabolic process / lipid catabolic process / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Rhodococcus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Caines, M.E.C. / Strynadka, N.C.J. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2007 Title: The structural basis of glycosidase inhibition by five-membered iminocyclitols: the clan a glycoside hydrolase endoglycoceramidase as a model system. Authors: Caines, M.E. / Hancock, S.M. / Tarling, C.A. / Wrodnigg, T.M. / Stick, R.V. / Stutz, A.E. / Vasella, A. / Withers, S.G. / Strynadka, N.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oyk.cif.gz | 208.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oyk.ent.gz | 161.6 KB | Display | PDB format |
PDBx/mmJSON format | 2oyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oyk_validation.pdf.gz | 847 KB | Display | wwPDB validaton report |
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Full document | 2oyk_full_validation.pdf.gz | 849 KB | Display | |
Data in XML | 2oyk_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 2oyk_validation.cif.gz | 63.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/2oyk ftp://data.pdbj.org/pub/pdb/validation_reports/oy/2oyk | HTTPS FTP |
-Related structure data
Related structure data | 2oylC 2oymC 2oswS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
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-Components
#1: Protein | Mass: 52122.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: M-777 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Tuner) / References: UniProt: O33853, endoglycosylceramidase #2: Chemical | ChemComp-NA / #3: Sugar | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% (w/v) PEG 3350; 0.175 M NaCl; 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2006 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→53 Å / Num. obs: 146070 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 16.068 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.6 / Num. measured all: 155646 / Num. unique all: 21265 / Rsym value: 0.456 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OSW Resolution: 1.5→53 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.281 / SU ML: 0.049 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.219 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→53 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4994 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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