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- PDB-1un8: Crystal structure of the dihydroxyacetone kinase of C. freundii (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1un8 | ||||||
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Title | Crystal structure of the dihydroxyacetone kinase of C. freundii (native form) | ||||||
![]() | DIHYDROXYACETONE KINASE | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() glycerone kinase / anaerobic glycerol catabolic process / glycerone kinase activity / phosphorylation / lipid binding / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Siebold, C. / Arnold, I. / Garcia-Alles, L.F. / Baumann, U. / Erni, B. | ||||||
![]() | ![]() Title: Crystal Structure of the Citrobacter Freundii Dihydroxyacetone Kinase Reveals an Eight-Stranded Alpha-Helical Barrel ATP-Binding Domain Authors: Siebold, C. / Arnold, I. / Garcia-Alles, L.F. / Baumann, U. / Erni, 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 | ![]() | 211.7 KB | Display | ![]() |
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PDB format | ![]() | 171.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 851.3 KB | Display | ![]() |
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Full document | ![]() | 877.7 KB | Display | |
Data in XML | ![]() | 43.3 KB | Display | |
Data in CIF | ![]() | 59.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper: (Code: given Matrix: (0.05306, 0.9985, -0.01375), Vector: |
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Components
#1: Protein | Mass: 57992.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 50187 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.4 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 83.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 9.1 |
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Processing
Software | Name: REFMAC / Version: 5.1.19 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Details: RESIDUES 518 - 525 WERE NOT VISIBLE IN ELECTRON DENSITY. N-TERMINAL MET WAS MODELLED AS ALA.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.92 Å
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Refine LS restraints |
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