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- PDB-7uf5: RibB from Vibrio cholera bound with intermediate 2 in the reactio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uf5 | ||||||
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Title | RibB from Vibrio cholera bound with intermediate 2 in the reaction cycle and the products DHBP and formate | ||||||
![]() | 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 | ![]() | 99.3 KB | Display | ![]() |
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PDB format | ![]() | 69 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uezC ![]() 7uf0C ![]() 7uf1C ![]() 7uf2C ![]() 7uf3C ![]() 7uf4C ![]() 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 68 molecules ![](data/chem/img/N52.gif)
![](data/chem/img/N4O.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/N4O.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-N52 / ( |
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#3: Chemical | ChemComp-N4O / ( |
#4: Chemical | ChemComp-FMT / |
#5: Chemical | ChemComp-MN / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.61 % |
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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: 2.1→39.49 Å / Num. obs: 13068 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 32.63 Å2 / Rpim(I) all: 0.054 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.1→2.16 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1038 / Rpim(I) all: 0.351 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4P8E Resolution: 2.1→39.49 Å / SU ML: 0.2407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9166 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39.49 Å
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Refine LS restraints |
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LS refinement shell |
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