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- PDB-8uhz: X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex... -

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Basic information

Entry
Database: PDB / ID: 8uhz
TitleX-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with Mn2+
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 / protein O-linked glycosylation / carbohydrate binding / Golgi membrane / nucleotide binding / metal ion binding
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: 2.55 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 30, 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,72015
Polymers63,5141
Non-polymers1,20614
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.627, 65.012, 166.633
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: pPIC
Details (production host): His Tag (6x), c-Myc Epitope Tag, TEV 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.: 9 / 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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.67 %
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 MX300-HS / Detector: CCD / Date: Oct 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 22636 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 37.28 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.066 / Rrim(I) all: 0.182 / Net I/σ(I): 11.3
Reflection shellResolution: 2.57→2.61 Å / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1082 / CC1/2: 0.605 / CC star: 0.868 / Rpim(I) all: 0.458

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→29.66 Å / SU ML: 0.3266 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2287 1999 8.85 %
Rwork0.1803 20582 -
obs0.1845 22581 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.04 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 71 124 4343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264374
X-RAY DIFFRACTIONf_angle_d0.53725912
X-RAY DIFFRACTIONf_chiral_restr0.0416606
X-RAY DIFFRACTIONf_plane_restr0.0059769
X-RAY DIFFRACTIONf_dihedral_angle_d14.72431640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.620.31371240.27311280X-RAY DIFFRACTION86.08
2.62-2.690.32421410.25551432X-RAY DIFFRACTION99.68
2.69-2.770.32781350.2541450X-RAY DIFFRACTION99.87
2.77-2.860.32291530.23521466X-RAY DIFFRACTION100
2.86-2.960.27151390.20451458X-RAY DIFFRACTION100
2.96-3.080.26651360.19641465X-RAY DIFFRACTION99.94
3.08-3.220.24161410.20451478X-RAY DIFFRACTION100
3.22-3.390.2591450.20441454X-RAY DIFFRACTION99.94
3.39-3.60.27861400.17461494X-RAY DIFFRACTION100
3.6-3.880.19251460.15811487X-RAY DIFFRACTION99.94
3.88-4.260.17471440.14051489X-RAY DIFFRACTION99.94
4.27-4.880.14941490.12541494X-RAY DIFFRACTION99.94
4.88-6.140.2081470.16031531X-RAY DIFFRACTION99.94
6.14-29.660.21691590.18861604X-RAY DIFFRACTION99.72
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)
11.441548546871.36883362608-0.3552578531954.576727968420.2463784714643.77252213908-0.2921891763140.555149570033-0.246295653035-0.7890571248290.07147781958640.01447186498410.345130192567-0.05088908097950.1789451681020.265285530981-0.15649951924-0.005049565902020.478821698753-0.07188079555370.432954622008-27.9858252369-28.71183013419.0713451532
21.697844513230.609590912810.4865248590931.909355830790.6371379716391.80158097638-0.1900773664320.245571203546-0.0199318260081-0.2981908845620.1417362590850.117411778541-0.077630903974-0.09401691675130.04279659563960.256983888416-0.047670925495-0.02284329597280.2439144745830.01894079007190.251695806945-20.328016301-11.329285743928.6296516132
30.454760063733-0.3676104398360.93655806361.13460509432-0.6809143334662.15179605476-0.0256095450458-0.0239229075859-0.01445182009040.03868354073290.0284458200152-0.07463688458640.05071736564220.0463506695350.002463701335160.2658873919490.009925907421240.02392346566550.233655531416-0.01236522020780.281836749197-4.13970784634-15.055562387354.911506546
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 103 through 153 )103 - 1533 - 53
22chain 'A' and (resid 154 through 375 )154 - 37554 - 273
33chain 'A' and (resid 376 through 628 )376 - 628274 - 518

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