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Yorodumi- PDB-4zax: Structure of UbiX in complex with oxidised prenylated FMN (radical) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zax | ||||||
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Title | Structure of UbiX in complex with oxidised prenylated FMN (radical) | ||||||
Components | UbiXFlavin prenyltransferase (UbiX) | ||||||
Keywords | TRANSFERASE / prenyl transferase / flavin binding / UbiX | ||||||
Function / homology | Function and homology information flavin prenyltransferase / flavin prenyltransferase activity / prenyltransferase activity / carboxy-lyase activity Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | White, M.D. / Leys, D. | ||||||
Citation | Journal: Nature / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zax.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zax.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/4zax ftp://data.pdbj.org/pub/pdb/validation_reports/za/4zax | HTTPS FTP |
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-Related structure data
Related structure data | 4zafC 4zagC 4zalC 4zanC 4zavC 4zawC 4zayC 4zazC C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22384.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA4019 / Production host: Escherichia coli (E. coli) References: UniProt: Q9HX08, Lyases; Carbon-carbon lyases; Carboxy-lyases | ||||
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#2: Chemical | ChemComp-4LU / | ||||
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.64 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→42.75 Å / Num. obs: 29027 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.61→1.65 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→42.75 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.449 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / 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: 22.876 Å2
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Refinement step | Cycle: 1 / Resolution: 1.61→42.75 Å
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Refine LS restraints |
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