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Yorodumi- PDB-2w87: Xyl-CBM35 in complex with glucuronic acid containing disaccharide. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w87 | ||||||
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Title | Xyl-CBM35 in complex with glucuronic acid containing disaccharide. | ||||||
Components | ESTERASE D | ||||||
Keywords | HYDROLASE / PLANT CELL WALL DEGRADATION / CARBOHYDRATE PROTEIN BINDING / XYLAN / CMB35 / GLUCURONIC ACID | ||||||
Function / homology | Function and homology information feruloyl esterase activity / polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Montainer, C. / Bueren, A.L.v. / Dumon, C. / Flint, J.E. / Correia, M.A. / Prates, J.A. / Firbank, S.J. / Lewis, R.J. / Grondin, G.G. / Ghinet, M.G. ...Montainer, C. / Bueren, A.L.v. / 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. | ||||||
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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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w87.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w87.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/2w87 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w87 | HTTPS FTP |
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-Related structure data
Related structure data | 2vzpC 2vzqC 2vzrC 2w1wC 2w3jC 2w46SC 2w47C 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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-Components
#1: Protein | Mass: 14151.377 Da / Num. of mol.: 2 / Fragment: RESIDUES 160-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(STAR)DE3 References: UniProt: Q51815, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Chemical | ChemComp-CA / #3: Sugar | #4: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #5: Water | ChemComp-HOH / | Nonpolymer details | GLUCURONIC ACID CONTAINING DISACCHARIDE (GCU): SUGAR NOT CHARACTERISED. GLUCURONIC ACID CLEAR IN ...GLUCURONIC | |
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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 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 6.9 / Details: 20% PEG 3350, 0.4M THIOCYANATE PH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→24 Å / Num. obs: 30820 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.58→1.67 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.4 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W46 Resolution: 1.6→24.15 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.711 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.097 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→24.15 Å
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Refine LS restraints |
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