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- PDB-8uhv: X-ray crystal structure of Toxoplasma gondii Apo GalNAc-T3 -

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Basic information

Entry
Database: PDB / ID: 8uhv
TitleX-ray crystal structure of Toxoplasma gondii Apo GalNAc-T3
ComponentsGlycosyl transferase
KeywordsTRANSFERASE / GT-A fold GalNAc Glycosyltransferase / Mucin-type O-glycosylation / Toxoplasma gondii cyst wall glycosylation
Function / homology
Function and homology information


polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / carbohydrate binding / Golgi apparatus / membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Glycosyl transferase
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKumar, P. / Samara, N.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)1-ZIA-DE000754-03 United States
CitationJournal: Nat Commun / Year: 2024
Title: A Toxoplasma gondii O-glycosyltransferase that modulates bradyzoite cyst wall rigidity is distinct from host homologues.
Authors: Kumar, P. / Tomita, T. / Gerken, T.A. / Ballard, C.J. / Lee, Y.S. / Weiss, L.M. / Samara, N.L.
History
DepositionOct 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,37110
Polymers63,5141
Non-polymers8579
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.238, 67.281, 164.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Glycosyl transferase


Mass: 63514.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_318730 / Plasmid: pPICz-alpha
Details (production host): His Tag (6x), c-Myc Epitope Tag, TEV protease cleavage site
Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: A0A125YMZ8, polypeptide N-acetylgalactosaminyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5 and 14-20% PEG 8000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 28, 2022
RadiationMonochromator: FMB OXFORD single crystal side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 15357 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 52.8 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.077 / Rrim(I) all: 0.213 / Net I/σ(I): 9.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 7 % / Rmerge(I) obs: 1.204 / Num. unique obs: 726 / CC1/2: 0.554 / CC star: 0.84 / Rpim(I) all: 0.482 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUI1.20.1_4487data collection
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.63 Å / SU ML: 0.4116 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2369 746 4.87 %
Rwork0.1802 14563 -
obs0.1829 15309 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.42 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 56 24 4256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274389
X-RAY DIFFRACTIONf_angle_d0.53565939
X-RAY DIFFRACTIONf_chiral_restr0.0403611
X-RAY DIFFRACTIONf_plane_restr0.0052774
X-RAY DIFFRACTIONf_dihedral_angle_d14.43391642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.130.32111320.25532793X-RAY DIFFRACTION96.69
3.13-3.440.28831480.23312863X-RAY DIFFRACTION99.97
3.44-3.940.2381580.18292908X-RAY DIFFRACTION99.97
3.94-4.950.18361560.13782919X-RAY DIFFRACTION99.94
4.96-29.630.23871520.16983080X-RAY DIFFRACTION99.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.543942571860.287282449292-0.5153334831582.02892012723-0.3772287097692.31774386824-0.1583295758880.3254202095760.0275453843975-0.5466209542920.109700912132-0.09288434921450.006305104104750.09309902341750.04441228834850.401711945516-0.1002241786170.007747423260180.3523021067830.001091448835790.35416664032820.86743418215.817612718924.397234187
20.886060414921-0.859405792146-1.664117482472.083568447541.952186535124.05719008104-0.1447778035830.0600880370723-0.1382423855820.134880620562-0.07861441054960.1359727129750.104569583042-0.2019764307040.1937116303170.313413335863-0.0292179045124-0.01021533661290.2923003046120.03417172248870.3758602298955.965832778613.919470905852.6265862327
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 100 through 342 )100 - 3421 - 243
22chain 'A' and (resid 343 through 628 )343 - 628244 - 522

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