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Yorodumi- PDB-4ayl: Molecular structure of a metal-independent bacterial glycosyltran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ayl | ||||||
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Title | Molecular structure of a metal-independent bacterial glycosyltransferase that catalyzes the synthesis of histo-blood group A antigen | ||||||
Components | BOGT-METAL-INDEPENDENT GLYCOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / HISTO-BLOOD GROUP ENZYME | ||||||
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: 1.919 Å | ||||||
Authors | Thiyagarajan, N. / Pham, T.T.K. / Stinsonb, B. / Sundriyala, A. / Tumbale, P. / Lizotte-Waniewskib, M. / Brewb, K. / Acharya, K.R. | ||||||
Citation | Journal: Sci.Rep. / Year: 2012 Title: Structure of a Metal-Independent Bacterial Glycosyltransferase that Catalyzes the Synthesis of Histo-Blood Group a Antigen Authors: Thiyagarajan, N. / Pham, T.T.K. / Stinson, B. / Sundriyal, A. / Tumbale, P. / 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 | 4ayl.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ayl.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ayl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ayl_validation.pdf.gz | 427.3 KB | Display | wwPDB validaton report |
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Full document | 4ayl_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 4ayl_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 4ayl_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/4ayl ftp://data.pdbj.org/pub/pdb/validation_reports/ay/4ayl | HTTPS FTP |
-Related structure data
Related structure data | 4ayjC 2vs4S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29038.057 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-246 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 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-EPE / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 15 % (W/V) PEG 4000, CONTAINING 0.1 M TRIS, PH 7.5, 0.2 M CALCIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 20120 / % possible obs: 77.7 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 4.5 / % possible all: 22.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VS4 Resolution: 1.919→35.368 Å / SU ML: 0.5 / σ(F): 1.37 / Phase error: 23 / 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 / Bsol: 30.815 Å2 / ksol: 0.337 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.919→35.368 Å
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Refine LS restraints |
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LS refinement shell |
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