+Open data
-Basic information
Entry | Database: PDB / ID: 5mqm | |||||||||||||||
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Title | Glycoside hydrolase BT_0986 | |||||||||||||||
Components | Glycosyl hydrolases family 2, sugar binding domain | |||||||||||||||
Keywords | HYDROLASE / glycoside hydrolase / rhamnosidase / plant pectin / CAZy family 106 | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | |||||||||||||||
Authors | Basle, A. / Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Venditto, I. / Labourel, A. / Gilbert, H.J. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: Nature / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mqm.cif.gz | 421.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mqm.ent.gz | 341.7 KB | Display | PDB format |
PDBx/mmJSON format | 5mqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mqm_validation.pdf.gz | 478.7 KB | Display | wwPDB validaton report |
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Full document | 5mqm_full_validation.pdf.gz | 484.9 KB | Display | |
Data in XML | 5mqm_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 5mqm_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/5mqm ftp://data.pdbj.org/pub/pdb/validation_reports/mq/5mqm | HTTPS FTP |
-Related structure data
Related structure data | 5mqnC 5mqoC 5mqrC 5mqsC 5msxC 5msyC 5mt2C 5muiC 5mujC 5mwkC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 125135.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: Btheta7330_02599 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0FM19, UniProt: Q8A931*PLUS |
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-Non-polymers , 5 types, 331 molecules
#2: Chemical | #3: Chemical | ChemComp-RPQ / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 15% (w/v) PEG 550 MME, 15% (w/v) PEG 20000, 0.25 M rahmnose, 50mM hepes and 50 mm MOPS pH 7.56 6mM D-rhamnopyranose tetrazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→50.69 Å / Num. obs: 75602 / % possible obs: 98.9 % / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.11→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.548 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apo model Resolution: 2.11→50.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.428 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.183 / 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: 41.332 Å2
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Refinement step | Cycle: 1 / Resolution: 2.11→50.69 Å
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Refine LS restraints |
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