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- PDB-4cjc: orthorhombic crystal form of Bogt6a E192Q in complex with UDP-Gal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cjc | |||||||||
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Title | orthorhombic crystal form of Bogt6a E192Q in complex with UDP-GalNAc, UDP, GalNAc | |||||||||
![]() | GLYCOSYLTRANSFERASE FAMILY 6 | |||||||||
![]() | TRANSFERASE / ORTHORHOMBIC FORM / METAL-INDEPENDENT / HYDROLYSED PRODUCTS | |||||||||
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 | ![]() | 211.1 KB | Display | ![]() |
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PDB format | ![]() | 169.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 45.1 KB | Display | |
Data in CIF | ![]() | 57.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cj8C ![]() 4cjbSC 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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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: Chemical | #3: Chemical | #4: Sugar | Sequence details | WITH HIS-TAG | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 56.09 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 0.2 M LI2SO4, 0.1M BIS TRIS, PH 5.5, 20 % PEG 3350 |
-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: 3.42→88.8 Å / Num. obs: 17402 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 91.44 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 3.42→3.51 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CJB Resolution: 3.42→88.802 Å / SU ML: 0.57 / σ(F): 1.33 / Phase error: 33.16 / 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: 83.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.42→88.802 Å
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Refine LS restraints |
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LS refinement shell |
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