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Yorodumi- PDB-7q20: Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q20 | ||||||
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Title | Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98) in complex with blood group A trisaccharide | ||||||
Components | Ruminococcus gnavus endogalactosidase GH98 | ||||||
Keywords | HYDROLASE / endogalactosidase / glycoside hydrolase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ruminococcus gnavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Owen, C.D. / Wu, H. / Crost, E.H. / van Bakel, W. / Gascuena, A.M. / Latousakis, D. / Hicks, T. / Walpole, S. / Urbanowicz, P.A. / Ndeh, D. ...Owen, C.D. / Wu, H. / Crost, E.H. / van Bakel, W. / Gascuena, A.M. / Latousakis, D. / Hicks, T. / Walpole, S. / Urbanowicz, P.A. / Ndeh, D. / Monaco, S. / Salom, L.S. / Griffiths, R. / Colvile, A. / Spencer, D.I.R. / Walsh, M.A. / Angulo, J. / Juge, N. | ||||||
Funding support | 1items
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Citation | Journal: Plos Biol. / Year: 2021 Title: The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract. Authors: Wu, H. / Crost, E.H. / Owen, C.D. / van Bakel, W. / Martinez Gascuena, A. / Latousakis, D. / Hicks, T. / Walpole, S. / Urbanowicz, P.A. / Ndeh, D. / Monaco, S. / Sanchez Salom, L. / ...Authors: Wu, H. / Crost, E.H. / Owen, C.D. / van Bakel, W. / Martinez Gascuena, A. / Latousakis, D. / Hicks, T. / Walpole, S. / Urbanowicz, P.A. / Ndeh, D. / Monaco, S. / Sanchez Salom, L. / Griffiths, R. / Reynolds, R.S. / Colvile, A. / Spencer, D.I.R. / Walsh, M. / Angulo, J. / Juge, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q20.cif.gz | 691.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q20.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/7q20 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/7q20 | HTTPS FTP |
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-Related structure data
Related structure data | 7pmoC 7q1wC 4d6cS 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AG
#1: Protein | Mass: 94793.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9) (bacteria) Strain: ATCC 29149 / VPI C7-9 / Gene: RUMGNA_03119 / Production host: Escherichia coli (E. coli) / References: UniProt: A7B6A6 #2: Polysaccharide | |
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-Non-polymers , 4 types, 832 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.68 Å3/Da / Density % sol: 54.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 12.5% MPD; 25% PEG 1000; 12.5% PEG 3350, 0.1 M Sodium HEPES/MOPS pH 7.5, 30 mM magnesium chloride hexahydrate and 30 mM calcium chloride dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→108.411 Å / Num. obs: 145680 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.069 / Rrim(I) all: 0.172 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.748 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7011 / CC1/2: 0.394 / Rpim(I) all: 0.808 / Rrim(I) all: 1.931 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D6C Resolution: 1.95→108.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 10.008 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.812 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→108.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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