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- PDB-4zaf: Structure of UbiX in complex with oxidised FMN and dimethylallyl ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zaf | ||||||
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Title | Structure of UbiX in complex with oxidised FMN and dimethylallyl monophosphate | ||||||
![]() | Probable aromatic acid decarboxylase | ||||||
![]() | LYASE / prenyl transferase / flavin binding / UbiX | ||||||
Function / homology | ![]() flavin prenyltransferase / flavin prenyltransferase activity / prenyltransferase activity / carboxy-lyase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | White, M.D. / Leys, D. | ||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 61.9 KB | Display | ![]() |
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PDB format | ![]() | 43.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.9 KB | Display | ![]() |
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Full document | ![]() | 794.6 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zagC ![]() 4zalC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22384.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9HX08, Lyases; Carbon-carbon lyases; Carboxy-lyases |
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-Non-polymers , 5 types, 146 molecules ![](data/chem/img/4LR.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-4LR / | ||||
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#3: Chemical | ChemComp-FMN / | ||||
#4: Chemical | ChemComp-SCN / #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
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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: Jul 12, 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: 1.71→70.95 Å / Num. obs: 24314 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.71→1.75 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: This structure was solved using difference fourier Resolution: 1.71→70.95 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.77 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.082 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.416 Å2
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Refinement step | Cycle: 1 / Resolution: 1.71→70.95 Å
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Refine LS restraints |
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