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Open data
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Basic information
Entry | Database: PDB / ID: 5gv1 | ||||||
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Title | Crystal structure of ENZbleach xylanase wild type | ||||||
![]() | Endo-1,4-beta-xylanase | ||||||
![]() | HYDROLASE / Endo-1 / 4-beta-xylanase / GH11 xylanase | ||||||
Biological species | termite gut metagenome (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Crystal structure of ENZbleach xylanase wild type | ||||||
![]() | Chitnumsub, P. / Jaruwat, A. / Boonyapakorn, K. / Noytanom, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based protein engineering for thermostable and alkaliphilic enhancement of endo-beta-1,4-xylanase for applications in pulp bleaching Authors: Boonyapakron, K. / Jaruwat, A. / Liwnaree, B. / Nimchua, T. / Champreda, V. / Chitnumsub, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.1 KB | Display | ![]() |
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PDB format | ![]() | 54.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.3 KB | Display | ![]() |
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Full document | ![]() | 424.4 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gy8C ![]() 5gy9C ![]() 5gyaC ![]() 5gybC ![]() 5gycC ![]() 5gyeC ![]() 5gyfC ![]() 5gygC ![]() 5gyhC ![]() 5gyiC ![]() 1ig0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35842.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) termite gut metagenome (others) / Plasmid: pET28a / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | Residues (-35)-0 and 274-286 in the sample sequence are His-tag sequence. Residues 1-273 in the ...Residues (-35)-0 and 274-286 in the sample sequence are His-tag sequence. Residues 1-273 in the sample sequence is the xylanase protein. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.38 % / Mosaicity: 0.78 ° |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6.5 / Details: PEG 1500, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 14, 2013 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→30 Å / Num. obs: 38524 / % possible obs: 91 % / Redundancy: 2.27 % / Biso Wilson estimate: 10.184 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IG0 Resolution: 1.5→29.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.234 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.081 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.07 Å2 / Biso mean: 9.488 Å2 / Biso min: 4.81 Å2
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Refinement step | Cycle: final / Resolution: 1.5→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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