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- PDB-1iez: Solution Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Syntha... -

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Basic information

Entry
Database: PDB / ID: 1iez
TitleSolution Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase of Riboflavin Biosynthesis
Components3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase
KeywordsISOMERASE / dihydroxybutanone phosphate synthase / riboflavin biosynthesis / skeletal rearrangement / antimicrobial target / structure based design
Function / homology
Function and homology information


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 / protein homodimerization activity / identical protein binding / plasma membrane / cytosol
Similarity search - Function
DHBP synthase / 3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsKelly, M.J.S. / Ball, L.J. / Kuhne, R. / Bacher, A. / Oschkinat, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The NMR structure of the 47-kDa dimeric enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase and ligand binding studies reveal the location of the active site.
Authors: Kelly, M.J. / Ball, L.J. / Krieger, C. / Yu, Y. / Fischer, M. / Schiffmann, S. / Schmieder, P. / Kuhne, R. / Bermel, W. / Bacher, A. / Richter, G. / Oschkinat, H.
History
DepositionApr 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase


Theoretical massNumber of molelcules
Total (without water)23,3781
Polymers23,3781
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase / DHBP SYNTHASE / (DHBPS)S


Mass: 23378.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: P0A7J0, Isomerases; Intramolecular transferases; Transferring other groups

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141DQF-COSY

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Sample preparation

DetailsContents: 2mM DHBPS U-15N,13C, 50mmol NaPO4, pH 6, / Solvent system: 10%D2O, 90%H20
Sample conditionsIonic strength: 50mM NaPO4 / pH: 6.0 / Pressure: 1 atm / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ANSIG3Kraulisdata analysis
Azara3.3Boucherprocessing
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 730 NOE-derived distance constraints, 230 dihedral angle restraints, 40 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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