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- PDB-6qlj: Crystal structure of F181Q UbiX in complex with an oxidised N5-C1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qlj | |||||||||
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Title | Crystal structure of F181Q UbiX in complex with an oxidised N5-C1' adduct derived from DMAP | |||||||||
![]() | Flavin prenyltransferase UbiX | |||||||||
![]() | TRANSFERASE / UbiX Prenyltransferase Flavin binding | |||||||||
Function / homology | ![]() flavin prenyltransferase / flavin prenyltransferase activity / carboxy-lyase activity / nucleotide binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Marshall, S.A. / Leys, D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry. Authors: Marshall, S.A. / Payne, K.A.P. / Fisher, K. / White, M.D. / Ni Cheallaigh, A. / Balaikaite, A. / Rigby, S.E.J. / 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 | ![]() | 73 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761.5 KB | Display | ![]() |
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Full document | ![]() | 761.8 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qlgC ![]() 6qlhC ![]() 6qliC ![]() 6qlkC ![]() 6qllC ![]() 6qlvC ![]() 4zafS S: Starting model for refinement 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: 24777.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ubiX, C0044_29760, C8257_05245, CAZ10_26235, CGU42_07325, DT376_15100, DZ940_19110, DZ962_23875, NCTC13719_00955, PAERUG_E15_London_28_01_14_05236, PAMH19_1010, RW109_RW109_01660 Production host: ![]() ![]() |
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#2: Chemical | ChemComp-4LS / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: LMB screen (Molecular Dimensions) D7 15 % w/v PEG 3350, 0.1 M MES pH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50.16 Å / Num. obs: 23136 / % possible obs: 98.56 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.89 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.62 |
Reflection shell | Resolution: 1.77→1.83 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZAF Resolution: 1.77→50.16 Å / SU ML: 0.2231 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4997
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→50.16 Å
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Refine LS restraints |
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LS refinement shell |
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