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Yorodumi- PDB-1k49: Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k49 | ||||||
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Title | Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase (cation free form) | ||||||
Components | 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase | ||||||
Keywords | ISOMERASE / dihydroxybutanone phosphate synthase / riboflavin biosynthesis / 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 / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Magnaporthe grisea (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Liao, D.-I. / Zheng, Y.-J. / Viitanen, P.V. / Jordan, D.B. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase. Authors: Liao, D.I. / Zheng, Y.J. / Viitanen, P.V. / Jordan, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k49.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k49.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 1k49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k49_validation.pdf.gz | 380.1 KB | Display | wwPDB validaton report |
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Full document | 1k49_full_validation.pdf.gz | 386.2 KB | Display | |
Data in XML | 1k49_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1k49_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/1k49 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/1k49 | HTTPS FTP |
-Related structure data
Related structure data | 1k4iC 1k4lC 1k4oC 1k4pC 1g57S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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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Details | The biological assembly is a homodimer. Applying the following symmetry related operation on the coordinates of the monomer in the asymmetirc unit would generate the 2nd half of the dimer. rotation matrix -1.00000 0.00000 0.00000 0.00000 -1.00000 0.00000 0.00000 0.00000 1.00000 translation -1, -1, 0 |
-Components
#1: Protein | Mass: 25036.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe grisea (fungus) / Gene: rice blast fungi / Plasmid: PET-24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8TG90, Isomerases; Intramolecular transferases; Transferring other groups | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.54 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Li2SO4, MES-NaOH, PEG5000 Monomethyl ether, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Liao, D.-I., (2000) Acta Crystallogr, D56, 1495. / PH range low: 6.5 / PH range high: 6 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: MSC focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 30209 / Num. obs: 30209 / % possible obs: 88.6 % / Observed criterion σ(I): -3 / Redundancy: 3.65 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.5 / Num. unique all: 603 / % possible all: 36 |
Reflection | *PLUS Num. measured all: 110275 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: E. coli enzyme structure (1G57) Resolution: 1.5→30 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.201 / Lowest resolution: 15 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.4 |