+Open data
-Basic information
Entry | Database: PDB / ID: 4azw | ||||||
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Title | Crystal structure of monomeric WbdD. | ||||||
Components | WBDDWorld Blood Donor Day | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE | ||||||
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 / SYNCHROTRON / OTHER / Resolution: 2.47 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 | 4azw.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4azw.ent.gz | 149 KB | Display | PDB format |
PDBx/mmJSON format | 4azw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4azw ftp://data.pdbj.org/pub/pdb/validation_reports/az/4azw | 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
#1: Protein | Mass: 54153.969 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-458 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: ORF708 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47592 | ||
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#2: Chemical | ChemComp-ATP / | ||
#3: Chemical | ChemComp-SAM / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.3 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→67.7 Å / Num. obs: 18171 / % possible obs: 98.5 % / Observed criterion σ(I): 3.1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.3 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.47→67.73 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 16.916 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 42.122 Å2
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Refinement step | Cycle: LAST / Resolution: 2.47→67.73 Å
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