+Open data
-Basic information
Entry | Database: PDB / ID: 5olq | ||||||
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Title | Rhamnogalacturonan lyase | ||||||
Components | Rhamnogalacturonan lyase | ||||||
Keywords | LYASE / Pectin / PL9 / polysaccharide lyase family 9 / Rhamnogalacturonan lyase / endo-acting enzyme | ||||||
Function / homology | Function and homology information carbon-oxygen lyase activity, acting on polysaccharides / alpha-galactosidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Basle, A. / Luis, A.S. / Gilbert, H.J. | ||||||
Citation | Journal: Nat Microbiol / Year: 2018 Title: Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / ...Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / Venditto, I. / Ralet, M.C. / Henrissat, B. / Martens, E.C. / Mosimann, S.C. / Abbott, D.W. / 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 | 5olq.cif.gz | 558.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5olq.ent.gz | 454.3 KB | Display | PDB format |
PDBx/mmJSON format | 5olq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/5olq ftp://data.pdbj.org/pub/pdb/validation_reports/ol/5olq | HTTPS FTP |
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-Related structure data
Related structure data | 5olpC 5olrC 5olsC 5opjC 1ru4S S: Starting model for refinement 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 56980.395 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: HMPREF2534_01516 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A139KMS2, UniProt: Q8A051*PLUS #2: Chemical | #3: Chemical | #4: 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: 1.94 Å3/Da / Density % sol: 36.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mM sodium/potassium phosphate 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 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: 1.48→39.65 Å / Num. obs: 221195 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.48→1.51 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 10868 / CC1/2: 0.736 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RU4 Resolution: 1.48→39.65 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.218 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.059 / 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: 16.158 Å2
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Refinement step | Cycle: 1 / Resolution: 1.48→39.65 Å
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Refine LS restraints |
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