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- PDB-5c4b: Crystal structure of GTA + UDP-Glc + DI -

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Basic information

Entry
Database: PDB / ID: 5c4b
TitleCrystal structure of GTA + UDP-Glc + 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 / : / TRIETHYLENE GLYCOL / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsGagnon, S. / Meloncelli, P. / Zheng, R.B. / Haji-Ghassemi, O. / Johal, A.R. / Borisova, S. / 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: Data collection / Database references
Revision 1.3Mar 7, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _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.funding_organization
Revision 1.5Sep 27, 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: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8885
Polymers34,6941
Non-polymers1,1944
Water4,197233
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)71,77610
Polymers69,3882
Non-polymers2,3888
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7760 Å2
ΔGint-46 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.590, 149.280, 79.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 237 molecules

#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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
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: 1.54→74.74 Å / Num. obs: 44020 / % possible obs: 94.4 % / Redundancy: 4.48 % / Rmerge(I) obs: 0.042 / Χ2: 0.94 / Net I/σ(I): 15.5 / Num. measured all: 198528 / Scaling rejects: 1490
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.54-1.63.80.35131571241161.188789.1
1.6-1.663.910.2913.51638041651.1410090.8
1.66-1.734.050.2354.41729442381.112092.1
1.73-1.834.360.1755.71884942911.0715292.9
1.83-1.944.650.1297.92052943651.0322493.8
1.94-2.094.710.09112096744040.9524395.1
2.09-2.34.830.07113.82162944390.8418995.9
2.3-2.634.850.05218.82214545400.812696.7
2.63-3.314.820.03427.92243946300.7712098.2
3.31-19.854.650.02146.62258448320.7812999.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
d*TREK9.4SSIdata scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
CrystalClear1.3.6 SP2 r1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LZ0

1lz0


Resolution: 1.54→74.74 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.422 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 2219 5 %RANDOM
Rwork0.1827 ---
obs0.1841 41798 94.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.08 Å2 / Biso mean: 20.615 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 1.54→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 71 233 2655
Biso mean--22.02 29.23 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192536
X-RAY DIFFRACTIONr_bond_other_d0.0050.022420
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9873452
X-RAY DIFFRACTIONr_angle_other_deg0.9643.0025517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.695292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63322.712118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44315418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4121520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212754
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02612
X-RAY DIFFRACTIONr_mcbond_it1.2231.8891162
X-RAY DIFFRACTIONr_mcbond_other1.2061.8871161
X-RAY DIFFRACTIONr_mcangle_it1.8542.8271453
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 145 -
Rwork0.415 2891 -
all-3036 -
obs--88.77 %

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