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- PDB-5tjl: Crystal structure of GTA + A trisaccharide (mercury derivative) -

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Basic information

Entry
Database: PDB / ID: 5tjl
TitleCrystal structure of GTA + A trisaccharide (mercury derivative)
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / glycosyltransferases / histo blood group enzymes / product trisaccharide / GT-A fold
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 / : / Golgi cisterna membrane / : / 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 / : / Golgi cisterna membrane / : / 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: 1.89 Å
AuthorsLegg, M.S.G. / Gagnon, S.M.L. / Evans, S.V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-77655 Canada
CitationJournal: Glycobiology / Year: 2017
Title: High-resolution crystal structures and STD NMR mapping of human ABO(H) blood group glycosyltransferases in complex with trisaccharide reaction products suggest a molecular basis for product release.
Authors: Gagnon, S.M.L. / Legg, M.S.G. / Sindhuwinata, N. / Letts, J.A. / Johal, A.R. / Schuman, B. / Borisova, S.N. / Palcic, M.M. / Peters, T. / Evans, S.V.
History
DepositionOct 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0096
Polymers34,5651
Non-polymers1,4445
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)72,01812
Polymers69,1302
Non-polymers2,88810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6000 Å2
ΔGint-238 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.580, 150.660, 79.300
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: 34564.895 Da / Num. of mol.: 1 / Fragment: residues 64-354
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: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]octyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 641.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2112h-1b_1-5_1*OCCCCCCCC][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][hexyl]{[(1+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: The first crystals of GTA/GTB were grown as mercury derivatives (Patenaude, S.I., et al. 2002): 10 ul drops with 6-8 mg/ml protein, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) pH 7.5, ...Details: The first crystals of GTA/GTB were grown as mercury derivatives (Patenaude, S.I., et al. 2002): 10 ul drops with 6-8 mg/ml protein, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) pH 7.5, 50 mM, sodium acetate pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 5%(v/v) glycerol, 2%(w/v) PEG 4000, and 0.3-0.5 mM 3-chloromercuri-2-methoxypropylurea suspended over 1 ml of a resevoir solution: 50 mM ADA pH 7.5, 10 mM MnCl2, 100 mM ammonium sulfate, 5%(v/v) MPD, 10%(v/v) glycerol, and 8-10%(w/v) PEG 4000. Crystals were washed with artificial mother liquor ML-1 consisting of 10% polyethylene glycol (PEG) 4000, 30 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) buffer pH 7.5, 30 mM sodium acetate buffer pH 4.6, 100 mM ammonium sulfate, 10 mM MnCl2 and 30% glycerol as the cryoprotectant. Crystals of GTA/GTB in complex with the A and B trisaccharides were obtained by soaking them in mother liquor ML-1 with 30% glycerol and 45-50 mM substrates for 2-5 days at 18 degrees Celsius

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→19.92 Å / Num. obs: 25471 / % possible obs: 99.3 % / Redundancy: 4.74 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.89-1.964.560.3174.4199.9
1.96-2.044.550.2555.1199.9
2.04-2.134.670.1936.2199.8
2.13-2.244.70.1438.1199.8
2.24-2.384.750.10910.5199.8
2.38-2.564.790.08812.71100
2.56-2.824.830.067171100
2.82-3.234.840.04822.1199.9
3.23-4.064.870.03134.2198.8
4.06-19.924.790.03140195.3

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Processing

Software
NameVersionClassification
d*TREK8.0SSIdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LZ0

1lz0


Resolution: 1.89→19.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.04 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.131
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 1299 5.1 %RANDOM
Rwork0.1879 ---
obs0.1897 24171 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.47 Å2 / Biso mean: 31.273 Å2 / Biso min: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.78 Å20 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 1.89→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 46 86 2211
Biso mean--50.15 34.08 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192203
X-RAY DIFFRACTIONr_bond_other_d0.0020.022051
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9693014
X-RAY DIFFRACTIONr_angle_other_deg0.92434706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3122.97101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71115329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7391514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
X-RAY DIFFRACTIONr_mcbond_it1.393.0321044
X-RAY DIFFRACTIONr_mcbond_other1.393.0291043
X-RAY DIFFRACTIONr_mcangle_it2.084.5331303
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 100 -
Rwork0.26 1779 -
all-1879 -
obs--99.84 %

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