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Yorodumi- PDB-7zo0: Crystal structure of catalytic inactive unliganded form of FucOB,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zo0 | ||||||
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Title | Crystal structure of catalytic inactive unliganded form of FucOB, a GH95 family alpha-1,2-fucosidase from Akkermansia muciniphila | ||||||
Components | GH95 family alpha-1,2-fucosidase | ||||||
Keywords | HYDROLASE / Glycosyl hydrolase Fucosidase Akkermansia muciniphila Mucin Bombay blood group Blood conversion | ||||||
Function / homology | Alpha-L-fucosidase / Glycosyl hydrolase family 95, N-terminal domain / Glycosyl hydrolase family 65, N-terminal domain / alpha-L-fucosidase activity / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / Glycosyl hydrolase family 95 N-terminal domain-containing protein Function and homology information | ||||||
Biological species | Akkermansia muciniphila ATCC BAA-835 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Anso, I. / Cifuente, J.O. / Trastoy, B. / Guerin, M.E. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Turning universal O into rare Bombay type blood. Authors: Anso, I. / Naegeli, A. / Cifuente, J.O. / Orrantia, A. / Andersson, E. / Zenarruzabeitia, O. / Moraleda-Montoya, A. / Garcia-Alija, M. / Corzana, F. / Del Orbe, R.A. / Borrego, F. / Trastoy, ...Authors: Anso, I. / Naegeli, A. / Cifuente, J.O. / Orrantia, A. / Andersson, E. / Zenarruzabeitia, O. / Moraleda-Montoya, A. / Garcia-Alija, M. / Corzana, F. / Del Orbe, R.A. / Borrego, F. / Trastoy, B. / Sjogren, J. / Guerin, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zo0.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zo0.ent.gz | 124.4 KB | Display | PDB format |
PDBx/mmJSON format | 7zo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/7zo0 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/7zo0 | HTTPS FTP |
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-Related structure data
Related structure data | 7znzSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 87382.805 Da / Num. of mol.: 1 / Mutation: E541A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria) Strain: ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc Gene: Amuc_1120 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / References: UniProt: B2UR61 | ||||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM sodium chloride, 20% (w/v) PEG 3350 (PEG ION suite protein crystallization screening, Hampton Research) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→52.24 Å / Num. obs: 423928 / % possible obs: 99.84 % / Redundancy: 6.8 % / Biso Wilson estimate: 27.38 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1299 / Rpim(I) all: 0.05409 / Rrim(I) all: 0.1409 / Net I/σ(I): 12.84 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 43184 / CC1/2: 0.648 / CC star: 0.887 / Rpim(I) all: 0.4985 / Rrim(I) all: 1.323 / % possible all: 99.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZNZ Resolution: 1.95→52.24 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→52.24 Å
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Refine LS restraints |
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LS refinement shell |
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