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- PDB-6tep: Crystal structure of a galactokinase from Bifidobacterium infanti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tep | ||||||||||||
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Title | Crystal structure of a galactokinase from Bifidobacterium infantis in complex with ADP | ||||||||||||
![]() | Galactokinase | ||||||||||||
![]() | TRANSFERASE / ADP / complex / galactokinase | ||||||||||||
Function / homology | ![]() L-arabinokinase activity / galactokinase / galactokinase activity / galactose metabolic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 716.7 KB | Display | ![]() |
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PDB format | ![]() | 587.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 74.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6teqC ![]() 6terC ![]() 1pieS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 ADCB
#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.) ![]() Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12 Gene: Blon_2062 / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 1509 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES pH 6.0, 0.15 - 0.25 M NaCl and 18 - 22 % (w/v) polyethylene glycol 6000). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→94.58 Å / Num. obs: 336915 / % possible obs: 98.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.45→1.47 Å / Rmerge(I) obs: 0.663 / Num. unique obs: 16117 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PIE Resolution: 1.45→94.58 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.47 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.077 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Density insufficient to model residues 245-247 in chains A + B, 244-247 in chain C and 245 in chain D, as ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Density insufficient to model residues 245-247 in chains A + B, 244-247 in chain C and 245 in chain D, as well as the C-terminal His-tag in all chains.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.64 Å2 / Biso mean: 17.661 Å2 / Biso min: 5.94 Å2
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Refinement step | Cycle: final / Resolution: 1.45→94.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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