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Yorodumi- PDB-6teq: Crystal structure of a galactokinase from Bifidobacterium infanti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6teq | |||||||||
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Title | Crystal structure of a galactokinase from Bifidobacterium infantis in complex with 2-deoxy-2-fluoro-galactose | |||||||||
Components | Galactokinase | |||||||||
Keywords | TRANSFERASE / 2FGal / complex / galactokinase | |||||||||
Function / homology | Function and homology information L-arabinokinase activity / galactokinase / galactokinase activity / galactose metabolic process / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | |||||||||
Authors | Keenan, T. / Parmeggiani, F. / Fontenelle, C.Q. / Malassis, J. / Vendeville, J. / Offen, W.A. / Both, P. / Huang, K. / Marchesi, A. / Heyam, A. ...Keenan, T. / Parmeggiani, F. / Fontenelle, C.Q. / Malassis, J. / Vendeville, J. / Offen, W.A. / Both, P. / Huang, K. / Marchesi, A. / Heyam, A. / Young, C. / Charnock, S. / Davies, G.J. / Linclau, B. / Flitsch, S.L. / Fascione, M.A. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Cell Chem Biol / Year: 2020 Title: Profiling Substrate Promiscuity of Wild-Type Sugar Kinases for Multi-fluorinated Monosaccharides. Authors: Keenan, T. / Parmeggiani, F. / Malassis, J. / Fontenelle, C.Q. / Vendeville, J.B. / Offen, W. / Both, P. / Huang, K. / Marchesi, A. / Heyam, A. / Young, C. / Charnock, S.J. / Davies, G.J. / ...Authors: Keenan, T. / Parmeggiani, F. / Malassis, J. / Fontenelle, C.Q. / Vendeville, J.B. / Offen, W. / Both, P. / Huang, K. / Marchesi, A. / Heyam, A. / Young, C. / Charnock, S.J. / Davies, G.J. / Linclau, B. / Flitsch, S.L. / Fascione, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6teq.cif.gz | 738 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6teq.ent.gz | 608.7 KB | Display | PDB format |
PDBx/mmJSON format | 6teq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/6teq ftp://data.pdbj.org/pub/pdb/validation_reports/te/6teq | HTTPS FTP |
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-Related structure data
Related structure data | 6tepSC 6terC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45815.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Galactokinase with C-terminal His-tag Source: (gene. exp.) Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088 (bacteria) Gene: Blon_2062 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7GUI0 |
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-Sugars , 2 types, 8 molecules
#5: Sugar | ChemComp-GAF / #6: Sugar | ChemComp-2FG / |
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-Non-polymers , 7 types, 1615 molecules
#2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CL / #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.7 Å3/Da / Density % sol: 54.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.0, 0.25 M NaCl and 22 % (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.916 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→94.55 Å / Num. obs: 349052 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.44→1.46 Å / Rmerge(I) obs: 1.058 / Num. unique obs: 17309 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TEP Resolution: 1.44→94.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.435 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 122.64 Å2 / Biso mean: 18.964 Å2 / Biso min: 3.26 Å2
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Refinement step | Cycle: final / Resolution: 1.44→94.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.44→1.477 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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