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Open data
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Basic information
Entry | Database: PDB / ID: 5mqo | |||||||||||||||
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Title | Glycoside hydrolase BT_1003 | |||||||||||||||
![]() | Non-reducing end beta-L-arabinofuranosidase | |||||||||||||||
![]() | HYDROLASE / glycoside hydrolase / aceric acidase / plant pectin / CAZy family GH127 | |||||||||||||||
Function / homology | non-reducing end beta-L-arabinofuranosidase / beta-L-arabinofuranosidase activity / Beta-L-arabinofuranosidase, GH127 / Beta-L-arabinofuranosidase, GH127 catalytic domain / hydrolase activity, acting on glycosyl bonds / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / Glycoside hydrolase family 127 protein / Six-hairpin glycosidase![]() | |||||||||||||||
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 | ![]() | 247.9 KB | Display | ![]() |
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PDB format | ![]() | 200.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.5 KB | Display | ![]() |
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Full document | ![]() | 431 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mqmC ![]() 5mqnC ![]() 5mqrC ![]() 5mqsC ![]() 5msxC ![]() 5msyC ![]() 5mt2C ![]() 5muiC ![]() 5mujC ![]() 5mwkC ![]() 3wkxS ![]() 4qjyS 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: 78164.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hypBA1_2, Btheta7330_02619 / Plasmid: pET28b / Production host: ![]() ![]() References: UniProt: A0A0P0FFP9, UniProt: Q8A914*PLUS, non-reducing end beta-L-arabinofuranosidase |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 and 0.2 M potassium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.775 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→109.72 Å / Num. all: 143341 / Num. obs: 29265 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 4.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3300 / CC1/2: 0.339 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WKX, 4QJY Resolution: 2.5→109.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 31.661 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.252 / 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: 67.308 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→109.72 Å
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Refine LS restraints |
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