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Yorodumi- PDB-1iez: Solution Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Syntha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iez | ||||||
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Title | Solution Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase of Riboflavin Biosynthesis | ||||||
Components | 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase | ||||||
Keywords | ISOMERASE / dihydroxybutanone phosphate synthase / riboflavin biosynthesis / skeletal rearrangement / antimicrobial target / structure based design | ||||||
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 / protein homodimerization activity / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Kelly, M.J.S. / Ball, L.J. / Kuhne, R. / Bacher, A. / Oschkinat, H. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iez.cif.gz | 635 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iez.ent.gz | 527.7 KB | Display | PDB format |
PDBx/mmJSON format | 1iez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iez_validation.pdf.gz | 358.8 KB | Display | wwPDB validaton report |
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Full document | 1iez_full_validation.pdf.gz | 627 KB | Display | |
Data in XML | 1iez_validation.xml.gz | 78.1 KB | Display | |
Data in CIF | 1iez_validation.cif.gz | 106 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/1iez ftp://data.pdbj.org/pub/pdb/validation_reports/ie/1iez | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 2mM DHBPS U-15N,13C, 50mmol NaPO4, pH 6, / Solvent system: 10%D2O, 90%H20 |
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Sample conditions | Ionic strength: 50mM NaPO4 / pH: 6.0 / Pressure: 1 atm / Temperature: 313 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: 730 NOE-derived distance constraints, 230 dihedral angle restraints, 40 distance restraints from hydrogen bonds | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |