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- PDB-4frq: Crystal Structure of BBBB+UDP+Gal at pH 9.5 with MPD as the cryop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4frq | ||||||
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Title | Crystal Structure of BBBB+UDP+Gal at pH 9.5 with MPD as the cryoprotectant | ||||||
![]() | Histo-blood group ABO system transferase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johal, A.R. / Alfaro, J.A. / Blackler, R.J. / Schuman, B. / Borisova, S.N. / Evans, S.V. | ||||||
![]() | ![]() Title: pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state. Authors: Johal, A.R. / Blackler, R.J. / Alfaro, J.A. / Schuman, B. / Borisova, S. / Evans, S.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.3 KB | Display | ![]() |
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PDB format | ![]() | 98.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4fqwC ![]() 4fraC ![]() 4frbC ![]() 4frdC ![]() 4freC ![]() 4frhC ![]() 4frlC ![]() 4frmC ![]() 4froC ![]() 4frpC ![]() 4gbpC ![]() 4kxoC ![]() 3sxgS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/GAL.gif)
![](data/chem/img/GAL.gif)
#1: Protein | Mass: 34062.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: H6A2X0, UniProt: P16442*PLUS, ![]() |
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#5: Sugar | ChemComp-GAL / ![]() |
-Non-polymers , 4 types, 135 molecules ![](data/chem/img/UDP.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-UDP / ![]() |
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#3: Chemical | ChemComp-PEG / ![]() |
#4: Chemical | ChemComp-MN / |
#6: Water | ChemComp-HOH / ![]() |
-Details
Sequence details | THE ELECTRON DENSITY FOR RESIDUE 195 IS CONSISTENT |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.69 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM glycine, 30 mM sodium acetate with 20% MPD as cryoprotectant, pH 9.5, temperature 298K, ...Details: 1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM glycine, 30 mM sodium acetate with 20% MPD as cryoprotectant, pH 9.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 26, 2012 / Details: 9 CCDs, 9 TILED FIBER-OPTIC TAPERS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→50 Å / Num. obs: 12961 / % possible obs: 95.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 24.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3SXG Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0 / SU B: 7.078 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.272 / 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 mean: 24.542 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refine LS restraints |
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