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- PDB-4bqn: Structural insights into WcbI, a novel polysaccharide biosynthesi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bqn | ||||||
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Title | Structural insights into WcbI, a novel polysaccharide biosynthesis enzyme. Native protein. | ||||||
![]() | CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN | ||||||
![]() | TRANSFERASE / ACETYLTRANSFERASE / MELIOIDOSIS. | ||||||
Function / homology | ![]() Arc Repressor Mutant, subunit A - #2490 / Rossmann fold - #12080 / Polysaccharide biosynthesis enzyme WcbI / Polysaccharide biosynthesis enzyme WcbI / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vivoli, M. / Ayres, E. / Isupov, M.N. / Harmer, N.J. | ||||||
![]() | ![]() Title: Structural Insights Into Wcbi, a Novel Polysaccharide-Biosynthesis Enzyme. Authors: Vivoli, M. / Ayres, E. / Beaumont, E. / Isupov, M.N. / Harmer, N.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 342 KB | Display | ![]() |
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PDB format | ![]() | 295.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 62.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.995, 0.01996, 0.09785), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36098.941 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1053 molecules ![](data/chem/img/COA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 7 Details: 10% (W/V) PEG 8000, 75 MM LICL, 75 MM MGCL2, 0.05 M HEPES PH 7.0-8.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→24.15 Å / Num. obs: 397472 / % possible obs: 92.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 55.9 |
Reflection shell | Resolution: 1.38→1.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.7 / % possible all: 59.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.38→24.63 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.683 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→24.63 Å
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Refine LS restraints |
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