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Yorodumi- PDB-2w9x: The active site of a carbohydrate esterase displays divergent cat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w9x | ||||||
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Title | The active site of a carbohydrate esterase displays divergent catalytic and non-catalytic binding functions | ||||||
Components | PUTATIVE ACETYL XYLAN ESTERASE | ||||||
Keywords | HYDROLASE / CARBOHYDRATE ESTERASE FAMILY 2 / ACETYL XYLAN ESTERASE | ||||||
Function / homology | Function and homology information glucomannan catabolic process / acetylxylan esterase / acetylxylan esterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on glycosyl bonds / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Montanier, C. / Money, V.A. / Pires, V. / Flint, J.E. / Benedita, P.A. / Goyal, A. / Prates, J.A. / Izumi, A. / Stalbrand, H. / Morland, C. ...Montanier, C. / Money, V.A. / Pires, V. / Flint, J.E. / Benedita, P.A. / Goyal, A. / Prates, J.A. / Izumi, A. / Stalbrand, H. / Morland, C. / Cartmell, A. / Kolenova, K. / Topakas, E. / Dobson, E. / Bolam, D.N. / Davies, G.J. / Fontes, C.M. / Gilbert, H.J. | ||||||
Citation | Journal: Plos Biol. / Year: 2009 Title: The Active Site of a Carbohydrate Esterase Displays Divergent Catalytic and Noncatalytic Binding Functions. Authors: Montanier, C. / Money, V.A. / Pires, V. / Flint, J.E. / Benedita, P.A. / Goyal, A. / Prates, J.A. / Izumi, A. / Stalbrand, H. / Morland, C. / Cartmell, A. / Kolenova, K. / Topakas, E. / ...Authors: Montanier, C. / Money, V.A. / Pires, V. / Flint, J.E. / Benedita, P.A. / Goyal, A. / Prates, J.A. / Izumi, A. / Stalbrand, H. / Morland, C. / Cartmell, A. / Kolenova, K. / Topakas, E. / Dodson, E.J. / Bolam, D.N. / Davies, G.J. / Fontes, C.M. / 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 | 2w9x.cif.gz | 143.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w9x.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/2w9x ftp://data.pdbj.org/pub/pdb/validation_reports/w9/2w9x | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8324, 0.5539, -0.01636), |
-Components
#1: Protein | Mass: 40906.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3PDE5 #2: Chemical | ChemComp-GOL / #3: 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: 2.57 Å3/Da / Density % sol: 51.68 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.1 M IMIDAZOLE PH 8.0, 10% PEG 8000 |
-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: Apr 19, 2008 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→53.22 Å / Num. obs: 53120 / % possible obs: 100 % / Observed criterion σ(I): 0.03 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.62 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.156 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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