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Yorodumi- PDB-4w8b: Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w8b | ||||||||||||
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Title | Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library, in complex with XXLG | ||||||||||||
Components | Exo-xyloglucanase | ||||||||||||
Keywords | HYDROLASE / glycoside hydrolase / cell wall degrading enzyme / GH5 family | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | uncultured bacterium (environmental samples) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.15 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 | 4w8b.cif.gz | 203.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w8b.ent.gz | 158.4 KB | Display | PDB format |
PDBx/mmJSON format | 4w8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w8b_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4w8b_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4w8b_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 4w8b_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/4w8b ftp://data.pdbj.org/pub/pdb/validation_reports/w8/4w8b | HTTPS FTP |
-Related structure data
Related structure data | 4w84C 4w85C 4w86C 4w87C 4w88C 4w89C 4w8aC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42681.840 Da / Num. of mol.: 1 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: D2XML9 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[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)-alpha-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)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[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, 683 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.9 Å3/Da / Density % sol: 57.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: ammonium sulfate, sodium citrate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.954 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: 0.954 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→50 Å / Num. obs: 165780 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 11.637 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.056 / Χ2: 0.94 / Net I/σ(I): 26.38 / Num. measured all: 1377786 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 1.15→39.49 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.502 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.005 / ESU R Free: 0.005 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 176.06 Å2 / Biso mean: 9.959 Å2 / Biso min: 3.46 Å2
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Refinement step | Cycle: final / Resolution: 1.15→39.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.18 Å / Total num. of bins used: 20
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