+Open data
-Basic information
Entry | Database: PDB / ID: 4azt | ||||||
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Title | Co-crystal structure of WbdD and kinase inhibitor LY294002. | ||||||
Components | METHYLTRANSFERASE WBDD | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase / polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase / O antigen biosynthetic process / methyltransferase activity / methylation / protein kinase activity / phosphorylation / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.34 Å | ||||||
Authors | Hagelueken, G. / Huang, H. / Naismith, J.H. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2012 Title: Structure of Wbdd; a Bifunctional Kinase and Methyltransferase that Regulates the Chain Length of the O Antigen in Escherichia Coli O9A. Authors: Hagelueken, G. / Huang, H. / Clarke, B.R. / Lebl, T. / Whitfield, C. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4azt.cif.gz | 195.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4azt.ent.gz | 163.1 KB | Display | PDB format |
PDBx/mmJSON format | 4azt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4azt ftp://data.pdbj.org/pub/pdb/validation_reports/az/4azt | HTTPS FTP |
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-Related 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65063.023 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-556 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47592 |
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-Non-polymers , 5 types, 221 molecules
#2: Chemical | ChemComp-SAM / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-LY2 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.6 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5417 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→42.5 Å / Num. obs: 27997 / % possible obs: 99.3 % / Observed criterion σ(I): 2.4 / Redundancy: 8.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.1 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.34→112.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.451 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→112.42 Å
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Refine LS restraints |
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