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Yorodumi- PDB-4w88: Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w88 | |||||||||
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Title | Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with a xyloglucan oligosaccharide and TRIS | |||||||||
Components | Xyloglucan-specific endo-beta-1,4-glucanase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase / cell wall degrading enzyme / GH5 family | |||||||||
Function / homology | Function and homology information xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | uncultured bacterium (environmental samples) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | |||||||||
Authors | Santos, C.R. / Cordeiro, R.L. / Wong, D.W.S. / Murakami, M.T. | |||||||||
Funding support | Brazil, 1items
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Citation | Journal: Biochemistry / Year: 2015 Title: Structural Basis for Xyloglucan Specificity and alpha-d-Xylp(1 6)-d-Glcp Recognition at the -1 Subsite within the GH5 Family. Authors: Dos Santos, C.R. / Cordeiro, R.L. / Wong, D.W. / Murakami, M.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w88.cif.gz | 314.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w88.ent.gz | 255.2 KB | Display | PDB format |
PDBx/mmJSON format | 4w88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/4w88 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/4w88 | HTTPS FTP |
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-Related structure data
Related structure data | 4w84C 4w85C 4w86C 4w87C 4w89C 4w8aC 4w8bC 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
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 38423.809 Da / Num. of mol.: 2 / Fragment: unp residues 92-430 / Mutation: P166T Source method: isolated from a genetically manipulated source Details: cow's rumen Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli (E. coli) References: UniProt: D2K7Z0, xyloglucan-specific endo-beta-1,4-glucanase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-[beta-D-glucopyranose-(1-4)]beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 605 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, PEG400, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 139797 / % possible obs: 99.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 29.264 Å2 / Net I/σ(I): 10.43 |
Reflection shell | Resolution: 1.58→1.67 Å / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: native structure of XEG5A Resolution: 1.58→43.56 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.415 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.056 / 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: 24.744 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→43.56 Å
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Refine LS restraints |
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