+Open data
-Basic information
Entry | Database: PDB / ID: 2yg0 | ||||||||||||
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Title | CBM62 FROM CLOSTRIDIUM THERMOCELLUM XYL5A | ||||||||||||
Components | CARBOHYDRATE BINDING FAMILY 6 | ||||||||||||
Keywords | SUGAR BINDING PROTEIN | ||||||||||||
Function / homology | Galactose-binding domain-like / Jelly Rolls / Sandwich / Mainly Beta / : Function and homology information | ||||||||||||
Biological species | CLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Montanier, C.Y. / Correia, M.A.S. / Flint, J.E. / Zhu, Y. / Basle, A. / Mckee, L.S. / Prates, J.A.M. / Polizzi, S.J. / Coutinho, P.M. / Henrissat, B. ...Montanier, C.Y. / Correia, M.A.S. / Flint, J.E. / Zhu, Y. / Basle, A. / Mckee, L.S. / Prates, J.A.M. / Polizzi, S.J. / Coutinho, P.M. / Henrissat, B. / Fontes, C.M.G.A. / Gilbert, H.J. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: A Novel, Noncatalytic Carbohydrate-Binding Module Displays Specificity for Galactose-Containing Polysaccharides Through Calcium-Mediated Oligomerization. Authors: Montanier, C.Y. / Correia, M.A.S. / Flint, J.E. / Zhu, Y. / Basle, A. / Mckee, L.S. / Prates, J.A.M. / Polizzi, S.J. / Coutinho, P.M. / Lewis, R.J. / Henrissat, B. / Fontes, C.M.G.A. / Gilbert, H.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yg0.cif.gz | 48.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yg0.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 2yg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yg0_validation.pdf.gz | 837.1 KB | Display | wwPDB validaton report |
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Full document | 2yg0_full_validation.pdf.gz | 837.7 KB | Display | |
Data in XML | 2yg0_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 2yg0_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2yg0 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2yg0 | HTTPS FTP |
-Related structure data
Related structure data | 2yb7C 2yfuSC 2yfzC C: citing same article (ref.) S: Starting model for refinement |
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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: 16884.484 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING DOMAIN, RESIDUES 740-883 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: D1NNT8 |
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#2: Polysaccharide | alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-CA / |
#5: 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: 4.9 Å3/Da / Density % sol: 75 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 0.5 M AMMONIUM SULPHATE IN 0.1 M NA/HEPES, PH 7.4, CONTAINING 30% 2-METHYL-2,4-PENTANEDIOL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.073 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.073 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.93 Å / Num. obs: 28437 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YFU Resolution: 1.8→43.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.343 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.072 / 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: 17.721 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→43.98 Å
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Refine LS restraints |
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