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- PDB-6bjk: Human ABO(H) blood group glycosyltransferase GTB D302C mutant -

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Basic information

Entry
Database: PDB / ID: 6bjk
TitleHuman ABO(H) blood group glycosyltransferase GTB D302C mutant
ComponentsABO blood group (Transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)
KeywordsTRANSFERASE / Blood group transferases / glycosyltransferases / enzymes
Function / homology
Function and homology information


glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / ABO blood group biosynthesis / fucosylgalactoside 3-alpha-galactosyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / hexosyltransferase activity / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding ...glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / ABO blood group biosynthesis / fucosylgalactoside 3-alpha-galactosyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / 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 => GO:0016020
Similarity search - Function
Glycosyltransferase family 6 / Glycosyl transferase, 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 / MOLECULAR REPLACEMENT / Resolution: 2.12 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)34,3662
Polymers34,2741
Non-polymers921
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area13570 Å2
2
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)68,7314
Polymers68,5472
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5290 Å2
ΔGint-25 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.490, 150.260, 78.320
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 ABO blood group (Transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase) / ABO blood group (Transferase A / alpha 1-3-N-acetylgalactosaminyltransferase / transferase B / ...ABO blood group (Transferase A / alpha 1-3-N-acetylgalactosaminyltransferase / transferase B / alpha 1-3-galactosyltransferase)


Mass: 34273.613 Da / Num. of mol.: 1 / Fragment: UNP residues 54-344 / 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: D3HIC2, UniProt: P16442*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: small tubes
Details: Spontaneous crystals were recovered from concentrated stocks of GTB/D302C (55 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: Dec 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.12→19.58 Å / Num. obs: 17135 / % possible obs: 95.3 % / Redundancy: 4.68 % / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.088 / Χ2: 0.98 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsΧ2Diffraction-ID% possible all
2.12-2.24.560.2943.91.19198.8
2.2-2.284.560.2494.41.09198.3
2.28-2.394.580.2154.91.07197.9
2.39-2.514.660.1995.31.06197.4
2.51-2.674.670.1656.51196.8
2.67-2.884.750.1447.30.96195.9
2.88-3.164.730.1139.40.97195.4
3.16-3.624.730.08911.90.86193.8
3.62-4.554.680.06716.40.81191.6
4.55-19.584.870.05321.20.83187.5

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Processing

Software
NameVersionClassification
d*TREK9.4SSIdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
CrystalCleardata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LZ7
Resolution: 2.12→19.58 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.005 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.197 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 874 5.1 %RANDOM
Rwork0.1929 ---
obs0.1953 16261 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.39 Å2 / Biso mean: 35.243 Å2 / Biso min: 22.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2---1.4 Å20 Å2
3---3.19 Å2
Refinement stepCycle: final / Resolution: 2.12→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 6 122 2261
Biso mean--49.92 40.15 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192206
X-RAY DIFFRACTIONr_bond_other_d0.0020.022089
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9523003
X-RAY DIFFRACTIONr_angle_other_deg0.93634785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3625264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34222.673101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41515353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8081516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
X-RAY DIFFRACTIONr_mcbond_it1.3983.4541059
X-RAY DIFFRACTIONr_mcbond_other1.3873.4511058
X-RAY DIFFRACTIONr_mcangle_it2.2185.1661322
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 67 -
Rwork0.219 1239 -
all-1306 -
obs--98.72 %

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