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Yorodumi- PDB-4cjc: orthorhombic crystal form of Bogt6a E192Q in complex with UDP-Gal... -
+Open data
-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 | |||||||||
Components | GLYCOSYLTRANSFERASE FAMILY 6 | |||||||||
Keywords | TRANSFERASE / ORTHORHOMBIC FORM / METAL-INDEPENDENT / HYDROLYSED PRODUCTS | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3.42 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 | 4cjc.cif.gz | 211.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cjc.ent.gz | 169.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/4cjc ftp://data.pdbj.org/pub/pdb/validation_reports/cj/4cjc | HTTPS FTP |
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-Related structure data
Related structure data | 4cj8C 4cjbSC 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) / Plasmid: PET42B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 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: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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