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Yorodumi- PDB-4w8a: Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w8a | ||||||
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Title | Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library, in the native form | ||||||
Components | Exo-xyloglucanase | ||||||
Keywords | HYDROLASE / glycoside hydrolase / celll wall degrading enzyme / GH5 family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.72 Å | ||||||
Authors | Santos, C.R. / Cordeiro, R.L. / Wong, D.W.S. / Murakami, M.T. | ||||||
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 | 4w8a.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w8a.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 4w8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w8a_validation.pdf.gz | 438 KB | Display | wwPDB validaton report |
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Full document | 4w8a_full_validation.pdf.gz | 438.1 KB | Display | |
Data in XML | 4w8a_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 4w8a_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/4w8a ftp://data.pdbj.org/pub/pdb/validation_reports/w8/4w8a | HTTPS FTP |
-Related structure data
Related structure data | 4w84C 4w85C 4w86C 4w87C 4w88C 4w89C 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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Unit cell |
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-Components
#1: Protein | Mass: 42681.840 Da / Num. of mol.: 1 / Fragment: unp residues 139-516 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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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.88 % |
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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: 1.72→50 Å / Num. obs: 50907 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 17.562 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.046 / Χ2: 0.921 / Net I/σ(I): 45.99 / Num. measured all: 538560 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.72→42.28 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.525 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.07 / 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: 83.44 Å2 / Biso mean: 11.214 Å2 / Biso min: 4.47 Å2
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Refinement step | Cycle: final / Resolution: 1.72→42.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.743 Å / Total num. of bins used: 20
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