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- PDB-5bxc: Crystal structure of GTA + UDP + DI -

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Basic information

Entry
Database: PDB / ID: 5bxc
TitleCrystal structure of GTA + UDP + 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: 1.4 Å
AuthorsGagnon, S.
Funding support Canada, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Alberta Ingenuity Canada
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 8, 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 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water5,585310
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_654-x+1,y,-z-1/21
Buried area6860 Å2
ΔGint-54 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.650, 148.860, 80.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-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
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#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.: 310 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1 % PEG 4000, 4.5-5 % 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM N-[2-acetamido]-2-iminodiacetic acid (ADA), 30 mM sodium acetate, 5-8 mM cobalt chloride, pH 7.5

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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: 1.4→74.33 Å / Num. obs: 59210 / % possible obs: 95.1 % / Redundancy: 4.07 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 20.4
Reflection shellHighest resolution: 1.4 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.1 / % possible all: 81.4

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Processing

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

1lz0


Resolution: 1.4→74.33 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.998 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20061 3005 5.1 %RANDOM
Rwork0.18022 ---
obs0.18124 56204 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.449 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.4→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 53 310 2796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192597
X-RAY DIFFRACTIONr_bond_other_d0.0060.022473
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9763538
X-RAY DIFFRACTIONr_angle_other_deg0.9693.0025632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4385308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19622.439123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29115430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5781523
X-RAY DIFFRACTIONr_chiral_restr0.0870.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212875
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02644
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1121.7521205
X-RAY DIFFRACTIONr_mcbond_other1.111.751204
X-RAY DIFFRACTIONr_mcangle_it1.7642.6261510
X-RAY DIFFRACTIONr_mcangle_other1.7632.6281511
X-RAY DIFFRACTIONr_scbond_it1.6511.9471392
X-RAY DIFFRACTIONr_scbond_other1.6491.9471391
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.562.8442025
X-RAY DIFFRACTIONr_long_range_B_refined5.1915.6073204
X-RAY DIFFRACTIONr_long_range_B_other5.1915.6083205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.602 196 -
Rwork0.564 3337 -
obs--76.99 %

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