+Open data
-Basic information
Entry | Database: PDB / ID: 3pnl | ||||||
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Title | Crystal Structure of E.coli Dha kinase DhaK-DhaL complex | ||||||
Components | (PTS-dependent dihydroxyacetone kinase, ...) x 2 | ||||||
Keywords | TRANSFERASE / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Dha 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 / ADP binding / DNA damage response / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Shi, R. / McDonald, L. / Matte, A. / Cygler, M. / Ekiel, I. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase. Authors: Shi, R. / McDonald, L. / Cui, Q. / Matte, A. / Cygler, M. / Ekiel, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pnl.cif.gz | 227.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pnl.ent.gz | 188.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/3pnl ftp://data.pdbj.org/pub/pdb/validation_reports/pn/3pnl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | y, x, -z |
-Components
-PTS-dependent dihydroxyacetone kinase, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 38263.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1200, dhaK, JW5187, ycgT / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P76015, Transferases; Transferring phosphorus-containing groups |
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#2: Protein | Mass: 22666.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1199, dhaL, JW5186, ycgS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P76014, Transferases; Transferring phosphorus-containing groups |
-Non-polymers , 4 types, 200 molecules
#3: Chemical | ChemComp-GOL / | ||
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#4: Chemical | ChemComp-ADP / | ||
#5: Chemical | #6: 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: 3.07 Å3/Da / Density % sol: 59.89 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 3.5 M Sodium Formate, 0.1M Hepes pH 7.5, vapor diffusion, sitting drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Apr 15, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→49.92 Å / Num. obs: 38172 / % possible obs: 96.2 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.091 / Χ2: 0.997 / Net I/σ(I): 9.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.2044 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8206 / SU B: 11.148 / SU ML: 0.142 / SU R Cruickshank DPI: 0.238 / SU Rfree: 0.1918 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.42 Å2 / Biso mean: 46.2274 Å2 / Biso min: 25.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.202→2.259 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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