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Open data
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Basic information
Entry | Database: PDB / ID: 5msx | |||||||||||||||
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Title | Glycoside hydrolase BT_3662 | |||||||||||||||
![]() | Putative endo-1,4-beta-xylanase | |||||||||||||||
![]() | HYDROLASE / glycoside hydrolase / GH43 / arabinofuranosidase / plant pectin / RGII | |||||||||||||||
Function / homology | ![]() xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Basle, A. / Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Venditto, I. / Labourel, A. / Gilbert, H.J. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / ...Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / Field, R.A. / Zhu, Y. / O'Neill, M.A. / Urbanowicz, B.R. / York, W.S. / Davies, G.J. / Abbott, D.W. / Ralet, M.C. / Martens, E.C. / Henrissat, B. / Gilbert, H.J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 284.2 KB | Display | ![]() |
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PDB format | ![]() | 226.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mqmC ![]() 5mqnC ![]() 5mqoC ![]() 5mqrC ![]() 5mqsC ![]() 5msyC ![]() 5mt2C ![]() 5muiC ![]() 5mujC ![]() 5mwkC ![]() 3qz4S 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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 52234.000 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BT_3662 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 424 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/144.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/144.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EPE / | ||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-144 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% polyethylene glycol (PEG) 6000 and 0.1 M hepes pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.44 Å / Num. obs: 91827 / % possible obs: 99.4 % / Redundancy: 3.8 % / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.711 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QZ4 Resolution: 2.1→49.44 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.943 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.178 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.637 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→49.44 Å
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Refine LS restraints |
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