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- PDB-4zal: Structure of UbiX E49Q mutant in complex with reduced FMN and dim... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zal | ||||||
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Title | Structure of UbiX E49Q mutant in complex with reduced FMN and dimethylallyl monophosphate | ||||||
![]() | UbiX | ||||||
![]() | LYASE / prenyl transferase / UbiX / FMN binding | ||||||
Function / homology | ![]() flavin prenyltransferase / flavin prenyltransferase activity / prenyltransferase activity / carboxy-lyase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | White, M.D. / Leys, D. | ||||||
![]() | ![]() Title: UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis. Authors: White, M.D. / Payne, K.A. / Fisher, K. / Marshall, S.A. / Parker, D. / Rattray, N.J. / Trivedi, D.K. / Goodacre, R. / Rigby, S.E. / Scrutton, N.S. / Hay, S. / Leys, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.7 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817.1 KB | Display | ![]() |
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Full document | ![]() | 821.1 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zafC ![]() 4zagC ![]() 4zanC ![]() 4zavC ![]() 4zawC ![]() 4zaxC ![]() 4zayC ![]() 4zazC C: citing same article ( |
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Similar structure data |
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Links
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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
#1: Protein | Mass: 22383.756 Da / Num. of mol.: 1 / Mutation: E49Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9HX08, Lyases; Carbon-carbon lyases; Carboxy-lyases | ||
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#2: Chemical | ChemComp-4LR / | ||
#3: Chemical | ChemComp-FNR / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 12% PEG 3350, 150mM sodium thiocyanate, and 100mM Tris pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→42.84 Å / Num. obs: 28593 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rpim(I) all: 0.024 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.62→1.66 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.8 / Rpim(I) all: 0.292 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 26.468 Å2
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Refinement step | Cycle: 1 / Resolution: 1.62→42.84 Å
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Refine LS restraints |
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