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- PDB-6bji: Human ABO(H) blood group glycosyltransferase GTA D302C mutant -

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Basic information

Entry
Database: PDB / ID: 6bji
TitleHuman ABO(H) blood group glycosyltransferase GTA D302C mutant
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / Blood group transferases / glycosyltransferases / enzymes
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 / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion 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 / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region
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
Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsGagnon, S.M.L. / Legg, M.S.G. / Evans, S.V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-77655 Canada
CitationJournal: Glycobiology / Year: 2018
Title: Conserved residues Arg188 and Asp302 are critical for active site organization and catalysis in human ABO(H) blood group A and B glycosyltransferases.
Authors: Gagnon, S.M.L. / Legg, M.S.G. / Polakowski, R. / Letts, J.A. / Persson, M. / Lin, S. / Zheng, R.B. / Rempel, B. / Schuman, B. / Haji-Ghassemi, O. / Borisova, S.N. / Palcic, M.M. / Evans, S.V.
History
DepositionNov 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4042
Polymers34,3121
Non-polymers921
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area13710 Å2
2
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8084
Polymers68,6232
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area5520 Å2
ΔGint-26 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.580, 149.570, 79.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histo-blood group ABO system transferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N- ...Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Histo-blood group A transferase / A transferase / Histo-blood group B transferase / B transferase / NAGAT


Mass: 34311.664 Da / Num. of mol.: 1 / Fragment: UNP residues 64-354 / Mutation: D302C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli)
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 46.04 %
Crystal growTemperature: 277 K / Method: small tubes
Details: Spontaneous crystals were recovered from concentrated stocks of GTA/D302C (95-100 mg/mL) stored in 50 mM MOPS, pH 7.00, 0.1 M sodium chloride, 1 mM DTT, 5 mM manganese chloride, and kept at 277 K.

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→19.79 Å / Num. obs: 46171 / % possible obs: 98.7 % / Redundancy: 4.44 % / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.038 / Χ2: 0.98 / Net I/σ(I): 17.2 / Num. measured all: 206457 / Scaling rejects: 1549
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsΧ2Rejects% possible all
1.54-1.63.610.323.31671746081.2978100
1.6-1.663.720.2643.91724746211.2279100
1.66-1.733.880.2114.71804946221.16106100
1.73-1.834.140.1596.11933546361.11146100
1.83-1.944.520.1188.52130846561.0325599.7
1.94-2.094.670.087112184946320.9421599.6
2.09-2.34.830.072142245546140.8715599.2
2.3-2.634.940.04920.52295946280.8210298.4
2.63-3.315.030.0331.92318445910.798196.9
3.31-19.795.050.01954.62335445630.8133293.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
d*TREK9.4SSIdata scaling
PDB_EXTRACT3.2data extraction
CrystalCleardata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LZ0

1lz0


Resolution: 1.54→19.79 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.332 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 2329 5 %RANDOM
Rwork0.1811 ---
obs0.1824 43837 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.86 Å2 / Biso mean: 21.503 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.54→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 6 270 2514
Biso mean--24.93 33.5 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192314
X-RAY DIFFRACTIONr_bond_other_d0.0020.022149
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.953142
X-RAY DIFFRACTIONr_angle_other_deg0.95834951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66322.477109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86715380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5251519
X-RAY DIFFRACTIONr_chiral_restr0.0850.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212538
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 161 -
Rwork0.352 3248 -
all-3409 -
obs--99.88 %

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