+Open data
-Basic information
Entry | Database: PDB / ID: 4azs | ||||||
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Title | High resolution (2.2 A) crystal structure of WbdD. | ||||||
Components | METHYLTRANSFERASE WBDD | ||||||
Keywords | TRANSFERASE / KINASE | ||||||
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 / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.15 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 | 4azs.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4azs.ent.gz | 161.5 KB | Display | PDB format |
PDBx/mmJSON format | 4azs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4azs ftp://data.pdbj.org/pub/pdb/validation_reports/az/4azs | 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O9A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47592 |
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-Non-polymers , 5 types, 204 molecules
#2: Chemical | ChemComp-AMP / | ||||
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#3: Chemical | ChemComp-SAM / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | #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: 55.8 % / 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 / Wavelength: 0.9686 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→65 Å / Num. obs: 36526 / % possible obs: 100 % / Observed criterion σ(I): 3.2 / Redundancy: 11 % / Rmerge(I) obs: 0.09 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.15→65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.056 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 44.632 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→65 Å
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Refine LS restraints |
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