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- PDB-5gyb: Crystal structure of ENZbleach xylanase V5N+V6N+K7R+K223R+K227R a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gyb | ||||||
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Title | Crystal structure of ENZbleach xylanase V5N+V6N+K7R+K223R+K227R and T28C+T60C mutant | ||||||
![]() | 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 V5N+V6N+K7R+K223R+K227R and T28C+T60C mutant | ||||||
![]() | Chitnumsub, P. / Jaruwat, A. / Boonyapakorn, 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 | ![]() | 77.7 KB | Display | ![]() |
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PDB format | ![]() | 55 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.1 KB | Display | ![]() |
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Full document | ![]() | 425.3 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gv1SC ![]() 5gy8C ![]() 5gy9C ![]() 5gyaC ![]() 5gycC ![]() 5gyeC ![]() 5gyfC ![]() 5gygC ![]() 5gyhC ![]() 5gyiC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31675.787 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 1-273 in the sample sequence is the xylanase protein and V5N+V6N+K7R+K223R+K227R and ...Residues 1-273 in the sample sequence is the xylanase protein and V5N+V6N+K7R+K223R+K227R and T28C+T60C mutant. Residues at 274-281 are the His-tag sequence. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.36 % / Mosaicity: 0.618 ° |
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Crystal grow | Temperature: 298 K / Method: microbatch Details: PEG 3350, 0.1 M tri-sodium acetate pH 4.5, 0.1 M Bis-Tris pH 5.5 PH range: 4.5-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50.01 Å / Num. obs: 30620 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.027 / Net I/av σ(I): 41.315 / Net I/σ(I): 26.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 5GV1 Resolution: 1.65→50.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.907 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107 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: 75.32 Å2 / Biso mean: 16.198 Å2 / Biso min: 7.08 Å2
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Refinement step | Cycle: final / Resolution: 1.65→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.694 Å / Total num. of bins used: 20
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