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- PDB-3ioh: Crystal structure of the Fucosylgalactoside alpha N-acetylgalacto... -

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Basic information

Entry
Database: PDB / ID: 3ioh
TitleCrystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A)
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / GTA / ABO / cisAB mutant / AA(Gly)B / ROSSMANN FOLD / UNLIGANDED / OPEN CONFORMATION / BLOOD GROUP ANTIGEN / GLYCOPROTEIN / GLYCOSYLTRANSFERASE / GOLGI APPARATUS / MANGANESE / MEMBRANE / METAL-BINDING / POLYMORPHISM / SECRETED / SIGNAL-ANCHOR / TRANSMEMBRANE
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
Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsPesnot, T. / Jorgensen, R. / Palcic, M.M. / Wagner, G.K.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Structural and mechanistic basis for a new mode of glycosyltransferase inhibition.
Authors: Pesnot, T. / Jorgensen, R. / Palcic, M.M. / Wagner, G.K.
History
DepositionAug 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 13, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)34,7462
Polymers34,6541
Non-polymers921
Water6,828379
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)69,4924
Polymers69,3082
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5240 Å2
ΔGint-27 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.790, 148.610, 79.640
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-403-

HOH

21A-601-

HOH

31A-651-

HOH

DetailsThe biological assembly is a dimer with the second part generated by the two fold axis: -X, Y, -Z+1/2

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Components

#1: Protein Histo-blood group ABO system transferase / NAGAT / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / ...NAGAT / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase / Histo-blood group A transferase / A transferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Histo-blood group B transferase / B transferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form


Mass: 34654.008 Da / Num. of mol.: 1 / Fragment: Extracellular catalytic domain / Mutation: L266G, G268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: PCW DELTA 1AC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM MOPS pH 7, 50-200 mM ammonium sulfate, 50 mM MnCl2, and 6-9% PEG-3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2008 / Details: Mirrors
RadiationMonochromator: Double crystal Si[111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→74.329 Å / Num. obs: 86743 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 15.7
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.2 / Num. measured all: 77471 / Num. unique all: 12568 / Rsym value: 0.623 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.91 Å
Translation2.5 Å19.91 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASER1.3.3phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RIT

2rit


Resolution: 1.25→19.697 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.925 / SU ML: 0.06 / Isotropic thermal model: Anisotropic+isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.177 2621 3.02 %RANDOM
Rwork0.153 ---
obs0.153 86706 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.356 Å2 / ksol: 0.497 e/Å3
Displacement parametersBiso max: 128.94 Å2 / Biso mean: 22.607 Å2 / Biso min: 8.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.901 Å2-0 Å2-0 Å2
2---1.872 Å2-0 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 1.25→19.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 6 379 2708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014748
X-RAY DIFFRACTIONf_angle_d1.0818551
X-RAY DIFFRACTIONf_chiral_restr0.097358
X-RAY DIFFRACTIONf_plane_restr0.007710
X-RAY DIFFRACTIONf_dihedral_angle_d13.9591198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.25-1.2730.2451550.21143634518
1.273-1.2970.231360.19443574493
1.297-1.3240.2171330.18544074540
1.324-1.3520.1961550.16543764531
1.352-1.3840.181510.14943794530
1.384-1.4180.1521280.13643784506
1.418-1.4570.1681180.12844044522
1.457-1.50.1451400.11943814521
1.5-1.5480.1361200.11244354555
1.548-1.6030.1651240.11244204544
1.603-1.6680.1741330.11743914524
1.668-1.7430.1511330.11844184551
1.743-1.8350.1481380.11844494587
1.835-1.950.1521270.12144314558
1.95-2.1010.1521300.1244274557
2.101-2.3120.1391450.1244624607
2.312-2.6450.1761530.1344654618
2.645-3.330.1791470.14444874634
3.33-19.6990.1861550.18846554810

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