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- PDB-7uf3: RibB from Vibrio cholera bound with L-xylulose-5-phosphate (L-Xy5... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uf3 | ||||||
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Title | RibB from Vibrio cholera bound with L-xylulose-5-phosphate (L-Xy5P) and manganese | ||||||
![]() | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
![]() | LYASE / RibB / riboflavin / 3 / 4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Function / homology | ![]() GTP cyclohydrolase II activity / 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kenjic, N. / Meneely, K.M. / Lamb, A.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis. Authors: Kenjic, N. / Meneely, K.M. / Wherritt, D.J. / Denler, M.C. / Jackson, T.A. / Moran, G.R. / Lamb, A.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96 KB | Display | ![]() |
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PDB format | ![]() | 70.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 803.5 KB | Display | ![]() |
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Full document | ![]() | 804 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uezC ![]() 7uf0C ![]() 7uf1C ![]() 7uf2C ![]() 7uf4C ![]() 7uf5C ![]() 4p8eS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 23589.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ribB, D6U24_02240, ERS013198_00268, ERS013199_01247, ERS013202_00910, ERS013207_00669, FXE67_08125 Production host: ![]() ![]() References: UniProt: A0A0H6NPW4, 3,4-dihydroxy-2-butanone-4-phosphate synthase | ||||
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#2: Sugar | ChemComp-N3U / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M lithium acetate, 12-18% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.51 Å / Num. obs: 15092 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.26 Å2 / Rpim(I) all: 0.043 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2→2.05 Å / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1060 / Rpim(I) all: 0.256 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4P8E Resolution: 2→39.51 Å / SU ML: 0.1852 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.1933 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.51 Å
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Refine LS restraints |
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LS refinement shell |
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