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- PDB-5c38: Crystal structure of AABB + UDP-C-Gal + DI -

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Basic information

Entry
Database: PDB / ID: 5c38
TitleCrystal structure of AABB + 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 / : / Chem-URM / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 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: 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.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)35,7684
Polymers34,7261
Non-polymers1,0423
Water4,720262
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)71,5368
Polymers69,4522
Non-polymers2,0846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5400 Å2
ΔGint-40 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.510, 149.040, 79.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-728-

HOH

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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: 34726.070 Da / Num. of mol.: 1 / Fragment: UNP resdiues 64-354 / Mutation: L266M, G268A
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-URM / (((2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)methyl)phosphonic (((2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride / Uridine diphospho methylene galactopyranose


Mass: 564.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 1.45→19.88 Å / Num. obs: 55396 / % possible obs: 99.5 % / Redundancy: 4.26 % / Rmerge(I) obs: 0.043 / Χ2: 0.94 / Net I/σ(I): 15.9 / Num. measured all: 237687 / Scaling rejects: 1784
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.45-1.53.450.3083.21897554941.0814100
1.5-1.563.580.2553.91976755101.074699.9
1.56-1.633.750.2154.72064954851.0468100
1.63-1.723.960.17462204255261.03164100
1.72-1.834.340.1318.12420455150.97289100
1.83-1.974.530.09211.12543955500.91303100
1.97-2.174.660.0714.82612555510.87233100
2.17-2.484.750.051202662055690.8518799.9
2.48-3.124.790.03826.32694555870.8519399.3
3.12-19.884.750.02248.22692156090.8628796.5

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Processing

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

1lz0


Resolution: 1.45→6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.903 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 2811 5.1 %RANDOM
Rwork0.181 ---
obs0.1817 52585 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.09 Å2 / Biso mean: 14.088 Å2 / Biso min: 8.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.45→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 64 262 2554
Biso mean--17.18 25.96 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022398
X-RAY DIFFRACTIONr_bond_other_d0.0070.021633
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9983260
X-RAY DIFFRACTIONr_angle_other_deg0.923.0033902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31923.113106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45415382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4011515
X-RAY DIFFRACTIONr_chiral_restr0.2520.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212564
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02505
LS refinement shellResolution: 1.45→1.485 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 169 -
Rwork0.503 3451 -
all-3620 -
obs--99.94 %

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