+Open data
-Basic information
Entry | Database: PDB / ID: 4cjb | |||||||||
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Title | orthorhombic crystal form of Bogt6a E192Q in complex with GalNAc | |||||||||
Components | GLYCOSYLTRANSFERASE FAMILY 6 | |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information hexosyltransferase activity / carbohydrate metabolic process / nucleotide binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | BACTEROIDES OVATUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.78 Å | |||||||||
Authors | Pham, T. / Stinson, B. / Thiyagarajan, N. / Lizotte-Waniewski, M. / Brew, K. / Acharya, K.R. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structures of Complexes of a Metal-Independent Glycosyltransferase Gt6 from Bacteroides Ovatus with Udp-Galnac and its Hydrolysis Products. Authors: Pham, T.T.K. / Stinson, B. / Thiyagarajan, N. / Lizotte-Waniewski, M. / Brew, K. / Acharya, K.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cjb.cif.gz | 204.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cjb.ent.gz | 166.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/4cjb ftp://data.pdbj.org/pub/pdb/validation_reports/cj/4cjb | HTTPS FTP |
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-Related structure data
Related structure data | 4cj8C 4cjcC 4aylS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 29037.072 Da / Num. of mol.: 4 / Fragment: ACTIVE SITE, RESIDUES 1-246 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES OVATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A7LVT2, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase #2: Sugar | ChemComp-A2G / #3: Water | ChemComp-HOH / | Sequence details | WITH HIS-TAG | |
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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: 2.78 Å3/Da / Density % sol: 51.14 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 0.1M NA CITRATE, PH 5.0 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 289.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 3, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→67.63 Å / Num. obs: 29475 / % possible obs: 98 % / Observed criterion σ(I): 2.5 / Redundancy: 5.4 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 4AYL Resolution: 2.78→67.63 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 27.3 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.78→67.63 Å
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Refine LS restraints |
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LS refinement shell |
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