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- PDB-6gwy: Blood group synthase AAGlyB in its apo form cryoprotected with gl... -

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Basic information

Entry
Database: PDB / ID: 6gwy
TitleBlood group synthase AAGlyB in its apo form cryoprotected with glycerol
ComponentsABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)
KeywordsTRANSFERASE / blood group synthase / glycosyltransferase / dual specificity / cis-AB mutant
Function / homology
Function and homology information


fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / hexosyltransferase activity / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / hexosyltransferase activity / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region / membrane / metal ion binding
Similarity search - Function
Glycosyl transferase, family 6 / Glycosyltransferase family 6 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase) / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsRocha, J. / Royant, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BSV8-0011-02 France
CitationJournal: To be published
Title: Blood group synthase AAGlyB in its apo form cryoprotected with glycerol
Authors: Rocha, J. / Batot, G.O. / Palcic, M.M. / Breton, C. / Royant, A.
History
DepositionJun 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0265
Polymers34,6541
Non-polymers3724
Water6,684371
1
A: ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)
hetero molecules

A: ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,05310
Polymers69,3082
Non-polymers7458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6440 Å2
ΔGint-43 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.912, 149.300, 80.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-762-

HOH

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Components

#1: Protein ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)


Mass: 34654.008 Da / Num. of mol.: 1 / Mutation: L266G, G268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli) / References: UniProt: F0X360, UniProt: P16442*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS buffer, Magnesium chloride, ammonium sulfate and PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.4→42.34 Å / Num. obs: 62538 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rsym value: 0.086 / Net I/σ(I): 11.2
Reflection shellResolution: 1.4→1.42 Å / Rsym value: 0.748

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ZGG

3zgg


Resolution: 1.4→40 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.165 / SU ML: 0.037 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.054
RfactorNum. reflection% reflectionSelection details
Rfree0.16728 3222 5.2 %RANDOM
Rwork0.13144 ---
obs0.13327 59287 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.767 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-0 Å2
2---0.38 Å20 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 23 371 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.6483712
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86420.191157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03215472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4441527
X-RAY DIFFRACTIONr_chiral_restr0.1110.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022108
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9111.2431288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5291.8731655
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9671.5811427
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.99818.9254189
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.832715
X-RAY DIFFRACTIONr_sphericity_free25.6075254
X-RAY DIFFRACTIONr_sphericity_bonded14.33952755
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 229 -
Rwork0.223 4334 -
obs--99 %

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