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Yorodumi- PDB-7uf2: RibB from Vibrio cholera bound with D-xylulose-5-phosphate (D-Xy5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uf2 | ||||||
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Title | RibB from Vibrio cholera bound with D-xylulose-5-phosphate (D-Xy5P) and manganese | ||||||
Components | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | LYASE / RibB / riboflavin / 3 / 4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Function / homology | Function and homology information 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 | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kenjic, N. / Meneely, K.M. / Lamb, A.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uf2.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uf2.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 7uf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uf2_validation.pdf.gz | 766.5 KB | Display | wwPDB validaton report |
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Full document | 7uf2_full_validation.pdf.gz | 767.9 KB | Display | |
Data in XML | 7uf2_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 7uf2_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/7uf2 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/7uf2 | HTTPS FTP |
-Related structure data
Related structure data | 7uezC 7uf0C 7uf1C 7uf3C 7uf4C 7uf5C 4p8eS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 23589.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: ribB, D6U24_02240, ERS013198_00268, ERS013199_01247, ERS013202_00910, ERS013207_00669, FXE67_08125 Production host: Escherichia coli (E. coli) References: UniProt: A0A0H6NPW4, 3,4-dihydroxy-2-butanone-4-phosphate synthase | ||||
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#2: Sugar | ChemComp-5SP / | ||||
#3: Chemical | ChemComp-MN / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.36 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 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→39.55 Å / Num. obs: 15176 / % possible obs: 99.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.68 Å2 / Rpim(I) all: 0.043 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2→2.05 Å / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1092 / Rpim(I) all: 0.264 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4P8E Resolution: 2→39.55 Å / SU ML: 0.2197 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8453 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: 28.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.55 Å
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Refine LS restraints |
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LS refinement shell |
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