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- PDB-8ui1: X-ray crystal structure of Toxoplasma gondii GalNAc-T3 at pH 7.3 -

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Open data


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Basic information

Entry
Database: PDB / ID: 8ui1
TitleX-ray crystal structure of Toxoplasma gondii GalNAc-T3 at pH 7.3
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 / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5409
Polymers63,5141
Non-polymers1,0268
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.430, 65.713, 166.314
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

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Protein , 1 types, 1 molecules A

#1: Protein Glycosyl transferase


Mass: 63514.129 Da / Num. of mol.: 1 / Mutation: g297s
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_318730 / Production host: Komagataella pastoris (fungus)
References: UniProt: A0A125YMZ8, polypeptide N-acetylgalactosaminyltransferase

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Non-polymers , 5 types, 34 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Crystals were grown in buffer containing 0.1 M CHES pH 9.5 and 14-20% PEG 8000 (w/v) and soaked in cryo buffer containing 20% glycerol and HEPES pH 7.3.

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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: 2.9→30 Å / Num. obs: 15343 / % possible obs: 98 % / Redundancy: 6.7 % / Biso Wilson estimate: 63.88 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.074 / Rrim(I) all: 0.193 / Net I/σ(I): 11.8
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.204 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 727 / CC1/2: 0.297 / CC star: 0.677 / Rpim(I) all: 0.618 / Rrim(I) all: 1.363 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→29.68 Å / SU ML: 0.416 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.227 1541 10.08 %
Rwork0.1848 13748 -
obs0.1892 15289 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.23 Å2
Refinement stepCycle: LAST / Resolution: 2.91→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4163 0 63 26 4252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324395
X-RAY DIFFRACTIONf_angle_d0.61355955
X-RAY DIFFRACTIONf_chiral_restr0.0413611
X-RAY DIFFRACTIONf_plane_restr0.0096775
X-RAY DIFFRACTIONf_dihedral_angle_d15.91841636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-30.35911330.33391180X-RAY DIFFRACTION93.52
3-3.110.36271280.27591191X-RAY DIFFRACTION95.17
3.11-3.230.33011320.25861211X-RAY DIFFRACTION96.69
3.23-3.380.32041420.24631255X-RAY DIFFRACTION99.57
3.38-3.560.28451400.24051248X-RAY DIFFRACTION99.64
3.56-3.780.25071370.1881274X-RAY DIFFRACTION99.51
3.78-4.070.21641450.15881252X-RAY DIFFRACTION99.22
4.07-4.480.17351410.13931260X-RAY DIFFRACTION97.63
4.48-5.130.15861470.131231X-RAY DIFFRACTION96.43
5.13-6.450.18811470.16841303X-RAY DIFFRACTION99.25
6.45-29.680.20891490.17351343X-RAY DIFFRACTION96.82
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)
11.291646131090.3966626293110.6947473468141.02956446001-0.5725795652851.50596938826-0.1231599117070.222647928620.357213033319-0.494448951115-0.0436197746059-0.349108503871-0.130579777008-0.01163842470770.1334113667340.466941489262-0.1281702223280.06878864362280.6015196559570.03681218077040.64994536179327.481146873728.647051361719.0974930616
20.855045853960.174258357892-0.3482270681321.19302389664-0.2667554813721.62851499857-0.1905311937060.1518294695230.0876851458718-0.2894288373550.146574070964-0.1541653900420.162698746235-0.04429848360440.02447776457030.369382893107-0.08565353367220.009123468342090.394314144932-0.009412062320370.40774060503620.178957517111.21219283928.4667278674
30.830433377245-0.494282492538-1.272985516070.9405232816550.6890782649222.56694537328-0.0923429047073-0.0327339478601-0.0560637698290.02101997014280.0252139676580.120517315243-0.0390704036999-0.06913306456270.04315722532390.353863632384-0.0147902678531-0.03378713877890.3218325843910.04897688047120.3926252103784.4757017199615.112274643154.7928429808
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 - 521

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