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Yorodumi- PDB-4udk: Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4udk | |||||||||
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Title | Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76 Angstrom from unknown human gut bacteria (Uhgb_MP) in complex with N-acetyl-D-glucosamine, beta-D-mannopyranose and inorganic phosphate | |||||||||
Components | (UHGB_MP) x 2 | |||||||||
Keywords | TRANSFERASE / GLYCOSIDE HYDROLASE FAMILY 130 / B-1 / 4-MANNOPYRANOSYL-CHITOBIOSE PHOSPHORYLASE / N-GLYCAN PHOSPHOROLYSIS | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | UNCULTURED ORGANISM (environmental samples) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | |||||||||
Authors | Ladeveze, S. / Cioci, G. / Potocki-Veronese, G. / Tranier, S. / Mourey, L. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural Bases for N-Glycan Processing by Mannoside Phosphorylase. Authors: Ladeveze, S. / Cioci, G. / Roblin, P. / Mourey, L. / Tranier, S. / Potocki-Veronese, G. #1: Journal: J.Biol.Chem. / Year: 2013 Title: Role of Glycoside Phosphorylases in Mannose Foraging by Human Gut Bacteria. Authors: Ladeveze, S. / Tarquis, L. / Cecchini, D.A. / Bercovici, J. / Andre, I. / Topham, C.M. / Morel, S. / Laville, E. / Monsan, P. / Lombard, V. / Henrissat, B. / Potocki-Veronese, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4udk.cif.gz | 811.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4udk.ent.gz | 675.5 KB | Display | PDB format |
PDBx/mmJSON format | 4udk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/4udk ftp://data.pdbj.org/pub/pdb/validation_reports/ud/4udk | HTTPS FTP |
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-Related structure data
Related structure data | 4udgC 4udiSC 4udjC C: citing same article (ref.) S: Starting model for refinement |
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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 , 2 types, 6 molecules ABCDFE
#1: Protein | Mass: 39321.422 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) UNCULTURED ORGANISM (environmental samples) Description: FECAL SAMPLE FROM HOMO SAPIENS / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI References: UniProt: D9ZDQ9, Transferases; Glycosyltransferases; Hexosyltransferases #2: Protein | | Mass: 39335.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) UNCULTURED ORGANISM (environmental samples) Description: FECAL SAMPLE FROM HOMO SAPIENS / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-AI References: UniProt: D9ZDQ9, Transferases; Glycosyltransferases; Hexosyltransferases |
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-Sugars , 2 types, 12 molecules
#4: Sugar | ChemComp-BMA / #5: Sugar | ChemComp-NDG / |
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-Non-polymers , 6 types, 1226 molecules
#3: Chemical | ChemComp-PO4 / #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-K / #9: Chemical | #10: 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: 2.11 Å3/Da / Density % sol: 41.75 % / Description: NONE |
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Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 17.5% PEG 3350, 200 MM NH4CL, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014 / Details: PAIR OF KB MIRRORS FOR ADJUSTABLE FOCUSING |
Radiation | Monochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR (CINEL), CRYOCOOLED, 6MM GAP Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→45 Å / Num. obs: 197652 / % possible obs: 99.6 % / Observed criterion σ(I): -1 / Redundancy: 9.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.76→1.86 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.54 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UDI Resolution: 1.76→108.17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.449 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE-CHAIN ATOMS WERE REMOVED FROM THE STRUCTURE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→108.17 Å
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