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Yorodumi- PDB-2wyh: Structure of the Streptococcus pyogenes family GH38 alpha-mannosidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wyh | ||||||
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Title | Structure of the Streptococcus pyogenes family GH38 alpha-mannosidase | ||||||
Components | ALPHA-MANNOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / GLYCOSIDE HYDROLASE | ||||||
Function / homology | Function and homology information alpha-mannosidase activity / mannose metabolic process / oligosaccharide catabolic process / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PYOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Suits, M.D.L. / Zhu, Y. / Taylor, E.J. / Zechel, D.L. / Gilbert, H.J. / Davies, G.J. | ||||||
Citation | Journal: Plos One / Year: 2010 Title: Structure and Kinetic Investigation of Streptococcus Pyogenes Family Gh38 Alpha-Mannosidase Authors: Suits, M.D.L. / Zhu, Y. / Taylor, E.J. / Zechel, D.L. / Gilbert, H.J. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wyh.cif.gz | 384.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wyh.ent.gz | 307.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wyh_validation.pdf.gz | 467.2 KB | Display | wwPDB validaton report |
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Full document | 2wyh_full_validation.pdf.gz | 479.5 KB | Display | |
Data in XML | 2wyh_validation.xml.gz | 68.7 KB | Display | |
Data in CIF | 2wyh_validation.cif.gz | 99.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/2wyh ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wyh | HTTPS FTP |
-Related 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: 105241.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 GAS / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99YP5, alpha-mannosidase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | Sequence details | THE FIRST 22 RESIDUES ARE A C3 PROTEASE CLEAVABLE AFFINITY TAG (MGSSHHHHHH | |
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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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 12 MG/ML PROTEIN WITH 100 MM TRIS, PH 8.5, 1.5 M (NH4)2SO4, 12% V/V GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 2, 2007 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 152396 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.95 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.9→127 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.185 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. DISORDERED REGION OF MOLECULE B (RESIDUES 156-164).
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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 mean: 15.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→127 Å
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Refine LS restraints |
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