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Yorodumi- PDB-4ax8: Medium resolution structure of the bifunctional kinase- methyltra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ax8 | |||||||||
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Title | Medium resolution structure of the bifunctional kinase- methyltransferase WbdD | |||||||||
Components | WBDDWorld Blood Donor Day | |||||||||
Keywords | TRANSFERASE / KINASE / 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 / SAD / Resolution: 3 Å | |||||||||
Authors | Hagelueken, G. / Huang, H. / Naismith, J.H. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Crystallization, Dehydration and Experimental Phasing of Wbdd, a Bifunctional Kinase and Methyltransferase from Escherichia Coli O9A. Authors: Hagelueken, G. / Huang, H. / Harlos, K. / Clarke, B.R. / 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 | 4ax8.cif.gz | 180.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ax8.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ax8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/4ax8 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/4ax8 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 65094.031 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) / Strain (production host): ROSETTA / References: UniProt: Q47592, UniProt: J7I4B7*PLUS | ||||
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#2: Chemical | ChemComp-SAM / | ||||
#3: Chemical | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-CL / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | Details: 0.26 M LITHIUM SULFATE, 0.1 M TRIS-HCL PH 8.4, 1.12 M AMMONIUM SULFATE, 5 MM SAM/MG/ATP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Type: DIAMOND / Wavelength: 0.9791 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 19185 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.8→2.85 Å / Mean I/σ(I) obs: 1.1 / % possible all: 97.5 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 3→68.32 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.899 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R Free: 0.357 / 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: 60.475 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→68.32 Å
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Refine LS restraints |
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