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- PDB-5m5d: 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: 5m5d | ||||||||||||||||||||||||
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Title | Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-D-glucal | ||||||||||||||||||||||||
![]() | Glycosyl hydrolase family 71 | ||||||||||||||||||||||||
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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 | ![]() | 189.2 KB | Display | ![]() |
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PDB format | ![]() | 148.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lyrC ![]() 5m03C ![]() 5m17C ![]() 5m3wC ![]() 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
#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: pET28a (+) / Production host: ![]() ![]() ![]() | ||||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-D-glucal![]() | ||||
#3: Chemical | ChemComp-EDO / ![]() #4: Chemical | ChemComp-ACT / | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 3 M sodium acetate, pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.07→76.85 Å / Num. obs: 172107 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.07→1.09 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.748 / Mean I/σ(I) obs: 0.6 / CC1/2: 0.33 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: modified 4UTF Resolution: 1.07→76.85 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.853 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / 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: 17.852 Å2
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Refinement step | Cycle: 1 / Resolution: 1.07→76.85 Å
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Refine LS restraints |
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