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Yorodumi- PDB-5nre: A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a3Ga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nre | |||||||||
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Title | A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - a3GalT in complex with lactose - a3GalT-LAT | |||||||||
Components | N-acetyllactosaminide alpha-1,3-galactosyltransferase | |||||||||
Keywords | TRANSFERASE / glycosyltransferase / GTA | |||||||||
Function / homology | Function and homology information N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / lipid glycosylation / Golgi cisterna membrane / glycosyltransferase activity / protein glycosylation / vesicle / carbohydrate metabolic process / Golgi apparatus / metal ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | |||||||||
Authors | Albesa-Jove, D. / Marina, A. / Sainz-Polo, M.A. / Guerin, M.E. | |||||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Structural Snapshots of alpha-1,3-Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases. Authors: Albesa-Jove, D. / Sainz-Polo, M.A. / Marina, A. / 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 | 5nre.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nre.ent.gz | 175.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nre_validation.pdf.gz | 745.5 KB | Display | wwPDB validaton report |
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Full document | 5nre_full_validation.pdf.gz | 748.7 KB | Display | |
Data in XML | 5nre_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 5nre_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/5nre ftp://data.pdbj.org/pub/pdb/validation_reports/nr/5nre | HTTPS FTP |
-Related structure data
Related structure data | 5nr9SC 5nrbC 5nrdC 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
#1: Protein | Mass: 34365.492 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 80-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GGTA1 / Production host: Escherichia coli (E. coli) References: UniProt: P14769, N-acetyllactosaminide 3-alpha-galactosyltransferase #2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose | #3: 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: 2.76 Å3/Da / Density % sol: 55.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.010 M beta-lactose, 0.02 M L-Na-glutamate, 0.02 M alanine (racemic), 0.02 M glycine, 0.02 M L-lysine (racemic), 0.02 M serine (racemic), 0.1 M Sodium HEPES-MOPS (acid) mix pH 7.5, 20% (v/v) ...Details: 0.010 M beta-lactose, 0.02 M L-Na-glutamate, 0.02 M alanine (racemic), 0.02 M glycine, 0.02 M L-lysine (racemic), 0.02 M serine (racemic), 0.1 M Sodium HEPES-MOPS (acid) mix pH 7.5, 20% (v/v) glycerol and 10% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→42.67 Å / Num. obs: 51440 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.67 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5436 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 5149 / CC1/2: 0.786 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NR9 Resolution: 1.98→57.391 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 26.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→57.391 Å
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Refine LS restraints |
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LS refinement shell |
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