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Open data
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Basic information
Entry | Database: PDB / ID: 4cjb | |||||||||
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Title | orthorhombic crystal form of Bogt6a E192Q in complex with GalNAc | |||||||||
![]() | GLYCOSYLTRANSFERASE FAMILY 6 | |||||||||
![]() | TRANSFERASE | |||||||||
Function / homology | ![]() hexosyltransferase activity / carbohydrate metabolic process / nucleotide binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pham, T. / Stinson, B. / Thiyagarajan, N. / Lizotte-Waniewski, M. / Brew, K. / Acharya, K.R. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.5 KB | Display | ![]() |
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PDB format | ![]() | 166.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.5 KB | Display | ![]() |
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Full document | ![]() | 488.4 KB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 49.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cj8C ![]() 4cjcC ![]() 4aylS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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.) ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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