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Yorodumi- PDB-2vzr: C-terminal CBM35 from Amycolatopsis orientalis exo-chitosanase Cs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vzr | ||||||
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Title | C-terminal CBM35 from Amycolatopsis orientalis exo-chitosanase CsxA in complex with glucuronic acid | ||||||
Components | EXO-BETA-D-GLUCOSAMINIDASEExo-1,4-beta-D-glucosaminidase | ||||||
Keywords | HYDROLASE / CBM / FAMILY 35 / CSXA / GLUCURONIC ACID | ||||||
Function / homology | Function and homology information exo-1,4-beta-D-glucosaminidase / exo-1,4-beta-D-glucosaminidase activity / chitin catabolic process / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | AMYCOLATOPSIS ORIENTALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.95 Å | ||||||
Authors | Lammerts van Bueren, A. / Boraston, A.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Evidence that Family 35 Carbohydrate Binding Modules Display Conserved Specificity But Divergent Function. Authors: Montanier, C. / Van Bueren, A.L. / Dumon, C. / Flint, J.E. / Correia, M.A. / Prates, J.A. / Firbank, S.J. / Lewis, R.J. / Grondin, G.G. / Ghinet, M.G. / Gloster, T.M. / Herve, C. / Knox, J.P. ...Authors: Montanier, C. / Van Bueren, A.L. / Dumon, C. / Flint, J.E. / Correia, M.A. / Prates, J.A. / Firbank, S.J. / Lewis, R.J. / Grondin, G.G. / Ghinet, M.G. / Gloster, T.M. / Herve, C. / Knox, J.P. / Talbot, B.G. / Turkenburg, J.P. / Kerovuo, J. / Brzezinski, R. / Fontes, C.M.G.A. / Davies, G.J. / Boraston, A.B. / 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 | 2vzr.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vzr.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/2vzr ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vzr | HTTPS FTP |
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-Related structure data
Related structure data | 2vzpC 2vzqC 2w1wC 2w3jC 2w46C 2w47C 2w87C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13027.171 Da / Num. of mol.: 2 / Fragment: RESIDUES 906-1032 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56F26 #2: Chemical | ChemComp-CA / #3: Sugar | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 49.3 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.71 Å / Num. obs: 18625 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.9 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.615 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.177 / 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: 18.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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