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Open data
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Basic information
Entry | Database: PDB / ID: 5m1b | ||||||
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Title | Crystal structure of C-terminally tagged apo-UbiD from E. coli | ||||||
![]() | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase | ||||||
![]() | LYASE / UbiD / decarboxylase / ubiquinone biosynthesis / prFMN binding | ||||||
Function / homology | ![]() 4-hydroxy-3-polyprenylbenzoate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | White, M. / Leys, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis. Authors: Marshall, S.A. / Fisher, K. / Ni Cheallaigh, A. / White, M.D. / Payne, K.A. / Parker, D.A. / Rigby, S.E. / 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 | ![]() | 537.4 KB | Display | ![]() |
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PDB format | ![]() | 450.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.5 KB | Display | ![]() |
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Full document | ![]() | 497 KB | Display | |
Data in XML | ![]() | 50.5 KB | Display | |
Data in CIF | ![]() | 68.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m1cC ![]() 5m1dC ![]() 5m1eC ![]() 2idbS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 56736.629 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ubiD, c4790 / Production host: ![]() ![]() References: UniProt: P0AAB5, 4-hydroxy-3-polyprenylbenzoate decarboxylase |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.22 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: Crystals grown in 0.1 mM SPG pH 8, 25 w/v PEG 1500 Crystals were cryo-protected using 10 PEG 400 in mother liquor followed by rapid cryocooling. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.044 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→29.9 Å / Num. obs: 51401 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 71.3 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 3.15→3.23 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IDB Resolution: 3.15→29.9 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.869 / SU B: 52.237 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.991 Å2
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Refinement step | Cycle: 1 / Resolution: 3.15→29.9 Å
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Refine LS restraints |
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