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- PDB-5lyr: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lyr | ||||||||||||||||||||||||
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Title | Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-noeuromycin | ||||||||||||||||||||||||
![]() | Glycosyl hydrolase family 71 | ||||||||||||||||||||||||
![]() | HYDROLASE / endomannanase endomannosidase GH99 noeuromycin hydrolase N-glycosylation glycosylation inhibitor inhibition shape charge | ||||||||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Petricevic, M. / Sobala, L.F. / Fernandes, P.Z. / Raich, L. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Sollogoub, M. / Rovira, C. ...Petricevic, M. / Sobala, L.F. / Fernandes, P.Z. / Raich, L. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Sollogoub, M. / Rovira, C. / Jimenez-Barbero, J. / Davies, G.J. / Williams, S.J. | ||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase. Authors: Petricevic, M. / Sobala, L.F. / Fernandes, P.Z. / Raich, L. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Sollogoub, M. / Jimenez-Barbero, J. / Rovira, C. / Davies, G.J. / Williams, S.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 | ![]() | 191.2 KB | Display | ![]() |
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PDB format | ![]() | 152.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475 KB | Display | ![]() |
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Full document | ![]() | 475.5 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m03C ![]() 5m17C ![]() 5m3wC ![]() 5m5dC ![]() 5mc8C ![]() 5melC ![]() 4utfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43933.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BXY_34140 / Plasmid: pET-28a(+) / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Sugar | ChemComp-MAN / | #4: Chemical | ChemComp-MNM / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 3 M sodium acetate, pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→76.73 Å / Num. obs: 134771 / % possible obs: 94.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.14→1.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 1.158 / Mean I/σ(I) obs: 0.7 / CC1/2: 0.387 / % possible all: 61.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UTF Resolution: 1.14→76.73 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.004 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.123 Å2
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Refinement step | Cycle: 1 / Resolution: 1.14→76.73 Å
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Refine LS restraints |
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