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Yorodumi- PDB-1oi3: X-ray structure of the dihydroxyacetone kinase from Escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oi3 | ||||||
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Title | X-ray structure of the dihydroxyacetone kinase from Escherichia coli | ||||||
Components | HYPOTHETICAL PROTEIN YCGT | ||||||
Keywords | KINASE / DIHYDROXYACETONE KINASE / YCGT | ||||||
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 / carbohydrate phosphorylation / transferase complex / 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 / carbohydrate phosphorylation / transferase complex / 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 / OTHER / Resolution: 2 Å | ||||||
Authors | Siebold, C. / Garcia-Alles, L.-F. / Erni, B. / Baumann, U. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: A Mechanism of Covalent Substrate Binding in the X-Ray Structure of Subunit K of the Escherichia Coli Dihydroxyacetone Kinase Authors: Siebold, C. / Garcia-Alles, L.-F. / Erni, B. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oi3.cif.gz | 146.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oi3.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oi3_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 1oi3_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 1oi3_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 1oi3_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oi3 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oi3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
NCS oper: (Code: given Matrix: (-0.99962, -0.02733, 0.00426), Vector: |
-Components
#1: Protein | Mass: 39532.609 Da / Num. of mol.: 2 / Fragment: DIHYDROXYACETONE BINDING SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PMSEH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WA2127 / References: UniProt: P76015, glycerone kinase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | BELONGS TO THE DIHYDROXYA | |
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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: 2.56 Å3/Da / Density % sol: 51.96 % |
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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 |
Detector | Details: OSMIC MIRRORS |
Radiation | Monochromator: NI FILTER / 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: 51496 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2→2.04 Å / Rmerge(I) obs: 0.1 / % possible all: 60.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2→19.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: RESIDUES 218 TO 222 WERE MODELED AS POLY-ALANINES DUE TO INSUFFICEIENT ELECTRON DENSITY FOR THE SIDE-CHAINS FOR THESE RESIDUES.
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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 |
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Refinement step | Cycle: LAST / Resolution: 2→19.73 Å
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Refine LS restraints |
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