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- PDB-5c36: Crystal structure of GTA + UDP-C-Gal + DI -

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Basic information

Entry
Database: PDB / ID: 5c36
TitleCrystal structure of GTA + UDP-C-Gal + DI
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / Glycosyltransferase Deoxyinhibitor ABO(H) Blood-Group System Complex
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
Chem-DA8 / : / URIDINE-5'-DIPHOSPHATE / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGagnon, S. / Meloncelli, P. / Zheng, R.B. / Haji-Ghassemi, O. / Johal, A.R. / Borisova, S.N. / Lowary, T.L. / Evans, S.V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-77655 Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: High Resolution Structures of the Human ABO(H) Blood Group Enzymes in Complex with Donor Analogs Reveal That the Enzymes Utilize Multiple Donor Conformations to Bind Substrates in a Stepwise Manner.
Authors: Gagnon, S.M. / Meloncelli, P.J. / Zheng, R.B. / Haji-Ghassemi, O. / Johal, A.R. / Borisova, S.N. / Lowary, T.L. / Evans, S.V.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.source / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)35,5764
Polymers34,6941
Non-polymers8823
Water4,161231
1
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)71,1518
Polymers69,3882
Non-polymers1,7636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6780 Å2
ΔGint-51 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.550, 149.070, 79.630
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: 34694.008 Da / Num. of mol.: 1 / Fragment: UNP 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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-DA8 / octyl 3-deoxy-2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-xylo-hexopyranoside / Alpha-L-Fucp-(1,2)-Beta-D-3-deoxy-Galp-O(CH2)7CH3


Mass: 422.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H38O9
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Grown in 1% polyethylene glycol (PEG) 4000, 4.5-5% 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM N-[-acetamido]-2-iminodiacetic acid (ADA), 30 mM ...Details: Grown in 1% polyethylene glycol (PEG) 4000, 4.5-5% 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM N-[-acetamido]-2-iminodiacetic acid (ADA), 30 mM sodium acetate, 5 mM manganese chloride. Grown 5-10 days.

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→19.91 Å / Num. obs: 45201 / % possible obs: 98.8 % / Redundancy: 4.53 % / Rmerge(I) obs: 0.042 / Χ2: 0.96 / Net I/σ(I): 16.2 / Num. measured all: 206174 / Scaling rejects: 1548
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.55-1.613.740.2873.91689244951.2180100
1.61-1.673.870.2334.51753545111.1661100
1.67-1.754.130.1985.41880745371.191100
1.75-1.844.450.14772038445371.0619099.9
1.84-1.954.620.1129211394517125699.8
1.95-2.14.710.08911.62167445390.9228299.5
2.1-2.314.830.0714.72201345210.8817799.2
2.31-2.654.920.05119.42246945430.8312598.5
2.65-3.3350.03328.72251844860.799997.3
3.33-19.9150.02148.92274345150.818794

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Processing

Software
NameVersionClassification
d*TREK9.4SSIdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
CrystalClear1.3.6 SP2 r1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LZ0

1lz0


Resolution: 1.55→6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.276 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 2291 5.1 %RANDOM
Rwork0.1763 ---
obs0.1781 42908 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.1 Å2 / Biso mean: 16.511 Å2 / Biso min: 9.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.51 Å20 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.55→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 53 231 2612
Biso mean--26.07 27.71 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022487
X-RAY DIFFRACTIONr_bond_other_d0.0020.021702
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9813387
X-RAY DIFFRACTIONr_angle_other_deg0.9143.0024089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97322.783115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89115407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9861519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02544
LS refinement shellResolution: 1.55→1.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 134 -
Rwork0.357 2794 -
all-2928 -
obs--99.86 %

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