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- PDB-6bjm: Human ABO(H) blood group glycosyltransferase GTB R188K mutant -

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Basic information

Entry
Database: PDB / ID: 6bjm
TitleHuman ABO(H) blood group glycosyltransferase GTB R188K 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


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 / MOLECULAR REPLACEMENT / Resolution: 1.45 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,1722
Polymers33,0801
Non-polymers921
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area13500 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)66,3454
Polymers66,1612
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5500 Å2
ΔGint-24 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.670, 149.670, 79.180
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: 33080.254 Da / Num. of mol.: 1 / Fragment: UNP residues 54-335 / Mutation: R188K
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.: 218 / 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: 45.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: GTB/R188K crystals were obtained by hanging drop vapor diffusion at 4 degrees C, where 3 uL of concentrated stock (66-68 mg/mL) was mixed with 1 uL of reservoir solution containing 0.3 M ...Details: GTB/R188K crystals were obtained by hanging drop vapor diffusion at 4 degrees C, where 3 uL of concentrated stock (66-68 mg/mL) was mixed with 1 uL of reservoir solution containing 0.3 M sodium acetate and 0.3 M sodium chloride.

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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: Oct 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→19.81 Å / Num. obs: 53903 / % possible obs: 96.6 % / Redundancy: 3.84 % / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.031 / Χ2: 0.97 / Net I/σ(I): 21 / Num. measured all: 208656 / Scaling rejects: 1565
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsΧ2Rejects% possible all
1.45-1.53.080.2833.41643353131.124696.2
1.5-1.563.170.2341695753371.063896.9
1.56-1.633.280.194.91770953871.035197.9
1.63-1.723.420.165.818847549816999.1
1.72-1.833.670.1287.82028555070.979499.4
1.83-1.974.080.09111.52256554940.9413798.8
1.97-2.174.230.0617.42312954250.9316997.5
2.17-2.484.410.0426.52389353750.9116496
2.48-3.124.540.02639.72426652910.8926894
3.12-19.814.560.01768.32457252760.9652990.4

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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 1LZ7

1lz7


Resolution: 1.45→74.74 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.074 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 2733 5.1 %RANDOM
Rwork0.189 ---
obs0.1897 51167 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.63 Å2 / Biso mean: 20.853 Å2 / Biso min: 11.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--0.38 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.45→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 6 218 2458
Biso mean--29.12 30.73 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192339
X-RAY DIFFRACTIONr_bond_other_d0.0020.022170
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9533181
X-RAY DIFFRACTIONr_angle_other_deg0.97535012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60722.804107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47315388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4841517
X-RAY DIFFRACTIONr_chiral_restr0.090.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212575
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02514
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 187 -
Rwork0.392 3733 -
all-3920 -
obs--96.08 %

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