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Open data
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Basic information
Entry | Database: PDB / ID: 5msy | |||||||||
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Title | Glycoside hydrolase BT_1012 | |||||||||
![]() | Glycoside hydrolase | |||||||||
![]() | HYDROLASE / glycoside hydrolase / Apiosidase / plant pectin / RGII | |||||||||
Function / homology | Putative collagen-binding domain / Putative collagen-binding domain of a collagenase / Putative glycohydrolase domain DUF4038 / Protein of unknown function (DUF4038) / Glycoside hydrolase superfamily / AMMONIA / PHOSPHATE ION / DUF4038 domain-containing protein![]() | |||||||||
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 | ![]() | 292 KB | Display | ![]() |
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PDB format | ![]() | 234.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.2 KB | Display | ![]() |
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Full document | ![]() | 462.3 KB | Display | |
Data in XML | ![]() | 50.3 KB | Display | |
Data in CIF | ![]() | 72 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mqmC ![]() 5mqnC ![]() 5mqoC ![]() 5mqrC ![]() 5mqsC ![]() 5msxC ![]() 5mt2C ![]() 5muiC ![]() 5mujC ![]() 5mwkC ![]() 3kzsS 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53843.148 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BT_1012 / Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NH3 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 40 % (v/v) MPD, 0.2 M ammonium phosphate and Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→38.95 Å / Num. obs: 106979 / % possible obs: 99.5 % / Redundancy: 10.7 % / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 11 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.529 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KZS Resolution: 2.3→38.95 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.087 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.18 / 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: 33.684 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→38.95 Å
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Refine LS restraints |
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