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- PDB-8c4a: Structural and interactional insights into the glideosome-associa... -

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Basic information

Entry
Database: PDB / ID: 8c4a
TitleStructural and interactional insights into the glideosome-associated connector from Toxoplasma gondii
ComponentsPutative anonymous antigen-1
KeywordsSTRUCTURAL PROTEIN / glideosome-associated connector (GAC) / Toxoplasma gondii
Function / homology
Function and homology information


Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Putative anonymous antigen-1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.675 Å
AuthorsKumar, A. / Morgan, R.M.L. / Matthews, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Imperial College London United Kingdom
Citation
Journal: Elife / Year: 2023
Title: Structural and regulatory insights into the glideosome-associated connector from Toxoplasma gondii.
Authors: Kumar, A. / Vadas, O. / Dos Santos Pacheco, N. / Zhang, X. / Chao, K. / Darvill, N. / Rasmussen, H.O. / Xu, Y. / Lin, G.M. / Stylianou, F.A. / Pedersen, J.S. / Rouse, S.L. / Morgan, M.L. / ...Authors: Kumar, A. / Vadas, O. / Dos Santos Pacheco, N. / Zhang, X. / Chao, K. / Darvill, N. / Rasmussen, H.O. / Xu, Y. / Lin, G.M. / Stylianou, F.A. / Pedersen, J.S. / Rouse, S.L. / Morgan, M.L. / Soldati-Favre, D. / Matthews, S.
#1: Journal: To Be Published
Title: Structural and interactional insights into the glideosome-associated connector from Toxoplasma gondii
Authors: Kumar, A. / Morgan, M.R. / Matthews, S.J.
History
DepositionJan 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_planes
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entry_details.has_protein_modification / _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative anonymous antigen-1


Theoretical massNumber of molelcules
Total (without water)274,3761
Polymers274,3761
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area94340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.078, 123.605, 221.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative anonymous antigen-1


Mass: 274375.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_051880 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6JYP1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: NA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795, 0.9796, 0.9722
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 21, 2022
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.97221
ReflectionResolution: 2.675→110.75 Å / Num. obs: 904519 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.993 / Net I/σ(I): 14.1
Reflection shellResolution: 2.675→2.771 Å / Num. unique obs: 9144 / CC1/2: 0.681 / CC star: 0.9 / % possible all: 99.42

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Processing

Software
NameVersionClassification
SHELXv97.2phasing
XDSv1data reduction
REFMACv5.0refinement
Cootv0.9model building
RefinementMethod to determine structure: MAD / Resolution: 2.675→110.75 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 --RANDOM
Rwork0.2095 ---
obs-92922 100 %-
Refinement stepCycle: LAST / Resolution: 2.675→110.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18664 0 0 112 18776

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