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Yorodumi- PDB-1uoe: Crystal structure of the dihydroxyacetone kinase from E. coli in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uoe | ||||||
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Title | Crystal structure of the dihydroxyacetone kinase from E. coli in complex with glyceraldehyde | ||||||
Components | DIHYDROXYACETONE KINASE | ||||||
Keywords | TRANSFERASE / KINASE | ||||||
Function / homology | Function and homology information monosaccharide catabolic process / glycerol to glycerone phosphate metabolic process / phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / ketone catabolic process / glycerone kinase activity / transferase complex / carbohydrate phosphorylation / glycerol catabolic process / pyruvate metabolic process ...monosaccharide catabolic process / glycerol to glycerone phosphate metabolic process / phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / ketone catabolic process / glycerone kinase activity / transferase complex / carbohydrate phosphorylation / glycerol catabolic process / pyruvate metabolic process / DNA damage response / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Siebold, C. / Garcia-Alles, L.F. / Luthi-Nyffeler, T. / Flukiger-Bruhwiler, K. / Burgi, H.-B. / Baumann, U. / Erni, B. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Phosphoenolpyruvate- and ATP-Dependent Dihydroxyacetone Kinases: Covalent Substrate-Binding and Kinetic Mechanism Authors: Garcia-Alles, L.F. / Siebold, C. / Luthi-Nyffeler, T. / Flukiger-Bruhwiler, K. / Schneider, P. / Burgi, H.-B. / Baumann, U. / Erni, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uoe.cif.gz | 143.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uoe.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 1uoe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uoe_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 1uoe_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 1uoe_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 1uoe_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/1uoe ftp://data.pdbj.org/pub/pdb/validation_reports/uo/1uoe | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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: (-0.99962, -0.02733, 0.00426), Vector: |
-Components
#1: Protein | Mass: 39531.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COVALENTLY MODIFIED HIS A230 AND B230 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P76015, glycerone kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | pH: 5 / Details: pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 54971 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.1 |
-Processing
Software | Name: REFMAC / Version: 5.1.19 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.157 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: RESIDUES A1 - A19 AND B1 - B19 ARE DISORDERED. LOOPS A205 - A217 AND B205 - B217 WERE ALS NOT VISIBLE IN THE ELECTRON DENSITY
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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: 17.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.65 Å
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Refine LS restraints |
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