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- PDB-8bt6: Crystal structure of Toxoplasma gondii glideosome-associated connector -

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Basic information

Entry
Database: PDB / ID: 8bt6
TitleCrystal structure of Toxoplasma gondii glideosome-associated connector
ComponentsPutative anonymous antigen-1
KeywordsPROTEIN BINDING / actin-binding protein / armadillo repeat / solenoid / pleckstrin-homology domain
Function / homologyArmadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / ACETATE ION / : / Putative anonymous antigen-1
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsHung, Y.F. / Kursula, I.
Funding support Finland, Norway, 4items
OrganizationGrant numberCountry
Academy of Finland Finland
Sigrid Juselius Foundation Finland
Jane and Aatos Erkko Foundation Finland
Norwegian Research Council Norway
CitationJournal: To Be Published
Title: Structure of Toxoplasma gondii glideosome-associated connector suggests a role as an elastic element to assist myosin A in generating force for gliding motility
Authors: Hung, Y.F. / Chen, Q. / Pires, I. / Rosenthal, P.B. / Kursula, I.
History
DepositionNov 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 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 / 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: Putative anonymous antigen-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,7764
Polymers291,6391
Non-polymers1373
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-0 kcal/mol
Surface area101180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.399, 146.661, 185.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Putative anonymous antigen-1


Mass: 291638.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGPRC2_312630 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A151HKA5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris, pH 8.4, 1.4 M potassium sodium tartrate, 50 mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→47.33 Å / Num. obs: 141753 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 55.78 Å2 / CC1/2: 1 / Net I/σ(I): 14.2
Reflection shellResolution: 2.33→2.39 Å / Num. unique obs: 10315 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33→47.33 Å / SU ML: 0.4152 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.3302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2718 7086 5 %
Rwork0.2294 134609 -
obs0.2315 141695 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.67 Å2
Refinement stepCycle: LAST / Resolution: 2.33→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19955 0 6 62 20023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002320240
X-RAY DIFFRACTIONf_angle_d0.526927430
X-RAY DIFFRACTIONf_chiral_restr0.03363236
X-RAY DIFFRACTIONf_plane_restr0.00423589
X-RAY DIFFRACTIONf_dihedral_angle_d14.7647475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.482290.42524361X-RAY DIFFRACTION98.86
2.36-2.380.45862360.40524484X-RAY DIFFRACTION99.96
2.38-2.410.43642330.38714441X-RAY DIFFRACTION99.91
2.41-2.440.41162350.3814459X-RAY DIFFRACTION99.94
2.44-2.480.4162330.36694420X-RAY DIFFRACTION99.94
2.48-2.510.42462330.35944416X-RAY DIFFRACTION99.89
2.51-2.550.37352340.34674460X-RAY DIFFRACTION99.98
2.55-2.580.35072360.32774475X-RAY DIFFRACTION99.98
2.58-2.620.36572330.32444420X-RAY DIFFRACTION99.96
2.62-2.670.39862340.30784457X-RAY DIFFRACTION99.96
2.67-2.710.32012360.30394475X-RAY DIFFRACTION99.96
2.71-2.760.37062340.30744446X-RAY DIFFRACTION99.79
2.76-2.820.40292340.3254456X-RAY DIFFRACTION99.89
2.82-2.870.34782340.31694446X-RAY DIFFRACTION99.96
2.87-2.940.37892340.30844447X-RAY DIFFRACTION99.91
2.94-30.32992370.29474501X-RAY DIFFRACTION99.96
3-3.080.37642350.28764455X-RAY DIFFRACTION99.98
3.08-3.160.36362350.28044476X-RAY DIFFRACTION99.98
3.16-3.260.33432360.27984473X-RAY DIFFRACTION99.96
3.26-3.360.32522360.26894493X-RAY DIFFRACTION99.96
3.36-3.480.29782350.264465X-RAY DIFFRACTION99.94
3.48-3.620.2912370.23984496X-RAY DIFFRACTION99.98
3.62-3.780.25392370.21554507X-RAY DIFFRACTION99.96
3.78-3.980.23732370.20224496X-RAY DIFFRACTION99.96
3.98-4.230.21322390.19154546X-RAY DIFFRACTION100
4.23-4.560.22142380.1744510X-RAY DIFFRACTION100
4.56-5.020.22172400.17414563X-RAY DIFFRACTION100
5.02-5.740.25292400.19084556X-RAY DIFFRACTION100
5.74-7.230.22322430.19924626X-RAY DIFFRACTION99.98
7.23-47.330.18242530.15934783X-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)
10.66810356110.298035742748-0.214688285770.612792014339-0.09225414932310.594099802025-0.04510005534870.209881296065-0.18332482329-0.06098660218210.0267732912519-0.02100039318690.00468459656872-0.1373040795480.02103367760550.4216595403430.0244502528617-0.006571232811580.788571648530.0269661479420.52155245878725.330342768554.78104727555.3200315853
21.33447787004-0.165882696613-0.2028347971610.13683692583-0.0818136905283-0.08901967093830.1610383627130.337385057704-0.225587330905-0.0916185916802-0.106291331449-0.0607293558558-0.03090134010730.0298674679901-0.05054159087530.6046940928870.115110784672-0.02698850873680.7653476444730.02381914342460.5116041269169.189151650673.859188089218.528855508
31.202705916690.2620997799810.01354810657820.773162186795-0.0267216429020.889972623427-0.0305617399194-0.0270500222739-0.1385434809030.03442908788240.136203247802-0.1017609513350.09063281943940.228931728492-0.08622321018780.3862187269670.0690266494378-0.01472654054070.7513081776440.04872762101820.58368265439875.13173436150.635542263769.7378547833
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 7 through 1381 )7 - 13811 - 1375
22chain 'A' and (resid 1382 through 2064 )1382 - 20641376 - 2058
33chain 'A' and (resid 2065 through 2639 )2065 - 26392059 - 2633

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