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- PDB-1k49: Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthas... -
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Open data
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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) | ||||||
![]() | 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liao, D.-I. / Zheng, Y.-J. / Viitanen, P.V. / Jordan, D.B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.8 KB | Display | ![]() |
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PDB format | ![]() | 40.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1k4iC ![]() 1k4lC ![]() 1k4oC ![]() 1k4pC ![]() 1g57S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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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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 |
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Components
#1: Protein | Mass: 25036.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8TG90, ![]() | ||
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#2: Chemical | ChemComp-SO4 / ![]() #3: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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 |