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Yorodumi- PDB-5ay7: A psychrophilic glycoside hydrolase family 10 endo-beta-1,4-xylanase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ay7 | ||||||
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Title | A psychrophilic glycoside hydrolase family 10 endo-beta-1,4-xylanase | ||||||
Components | xylanase | ||||||
Keywords | HYDROLASE / xylanase / GH10 / TIM-barrel fold | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Aegilops speltoides subsp. speltoides (goat grass) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å | ||||||
Authors | Zheng, Y. / Li, Y. / Liu, W. / Guo, R.T. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2016 Title: Structural insight into potential cold adaptation mechanism through a psychrophilic glycoside hydrolase family 10 endo-beta-1,4-xylanase. Authors: Zheng, Y. / Li, Y. / Liu, W. / Chen, C.C. / Ko, T.P. / He, M. / Xu, Z. / Liu, M. / Luo, H. / Guo, R.T. / Yao, B. / Ma, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ay7.cif.gz | 145.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ay7.ent.gz | 114.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ay7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ay7_validation.pdf.gz | 440.2 KB | Display | wwPDB validaton report |
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Full document | 5ay7_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 5ay7_validation.xml.gz | 26 KB | Display | |
Data in CIF | 5ay7_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/5ay7 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5ay7 | HTTPS FTP |
-Related 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: 41219.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aegilops speltoides subsp. speltoides (goat grass) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A140UHL2*PLUS, endo-1,4-beta-xylanase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 8.5 / Details: 0.1M Tris, pH 8.5, 0.2M Li2SO4, 30% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→25 Å / Num. obs: 42567 / % possible obs: 98.38 % / Redundancy: 3.2 % / Net I/σ(I): 21.9 |
-Processing
Software |
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Refinement | Resolution: 2.15→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.776 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.208 / 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: 56.53 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→25 Å
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Refine LS restraints |
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