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- PDB-4ozu: Crystal Structure of WD40 domain from Toxoplasma gondii coronin -

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Basic information

Entry
Database: PDB / ID: 4ozu
TitleCrystal Structure of WD40 domain from Toxoplasma gondii coronin
ComponentsCoronin
KeywordsSTRUCTURAL PROTEIN / WD40 repeat / Actin binding protein / Apicomplexan parasite
Function / homology
Function and homology information


Type of WD40 repeat / Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / DUF1899 / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site ...Type of WD40 repeat / Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / DUF1899 / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Coronin
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKallio, J.P. / Kursula, I.
CitationJournal: Faseb J. / Year: 2014
Title: Structure of Toxoplasma gondii coronin, an actin-binding protein that relocalizes to the posterior pole of invasive parasites and contributes to invasion and egress.
Authors: Salamun, J. / Kallio, J.P. / Daher, W. / Soldati-Favre, D. / Kursula, I.
History
DepositionFeb 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Mar 7, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_site / symmetry
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_site.details / _symmetry.Int_Tables_number
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coronin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6353
Polymers43,4541
Non-polymers1812
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.130, 82.510, 156.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

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Components

#1: Protein Coronin


Mass: 43454.297 Da / Num. of mol.: 1 / Fragment: WD40 domain (UNP residues 2-392)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CRN1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: Q5Y1E7
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PMME 2000, ammonium acetate, TRIS-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 43134 / % possible obs: 99.2 % / Redundancy: 3.9 % / Net I/σ(I): 12.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AQ5

2aq5


Resolution: 1.65→45.839 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 1999 4.63 %
Rwork0.1629 --
obs0.1647 43130 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→45.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3035 0 12 363 3410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053185
X-RAY DIFFRACTIONf_angle_d0.9674331
X-RAY DIFFRACTIONf_dihedral_angle_d12.661171
X-RAY DIFFRACTIONf_chiral_restr0.038470
X-RAY DIFFRACTIONf_plane_restr0.004565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.41491390.36042852X-RAY DIFFRACTION99
1.6913-1.7370.34831420.31652936X-RAY DIFFRACTION100
1.737-1.78810.31481420.262918X-RAY DIFFRACTION99
1.7881-1.84580.2741420.23472907X-RAY DIFFRACTION99
1.8458-1.91180.29811410.2212916X-RAY DIFFRACTION99
1.9118-1.98830.25891410.19622885X-RAY DIFFRACTION99
1.9883-2.07880.21971400.17382899X-RAY DIFFRACTION99
2.0788-2.18840.21221430.1662916X-RAY DIFFRACTION99
2.1884-2.32550.23421410.16192917X-RAY DIFFRACTION99
2.3255-2.50510.20721450.16152975X-RAY DIFFRACTION100
2.5051-2.75710.21321440.16652961X-RAY DIFFRACTION99
2.7571-3.1560.20341430.1592938X-RAY DIFFRACTION100
3.156-3.97590.14491450.13282992X-RAY DIFFRACTION99
3.9759-45.8570.16081510.12923119X-RAY DIFFRACTION99
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)
11.7840.12480.56472.98830.45861.16980.064-0.24890.31250.136-0.0670.2324-0.08640.0533-0.03730.2603-0.08090.06050.2619-0.03130.23940.6293-13.4169-15.6309
21.91710.87071.91461.70420.42282.7486-0.1269-0.06370.78680.03730.0440.5607-0.426-0.07650.07740.2554-0.01460.03030.20030.02480.5134-11.3959-7.1326-25.0799
31.69470.2420.13643.76350.67091.91350.00180.22960.5012-0.16660.02220.3877-0.2308-0.1315-0.04510.1759-0.0087-0.0220.22120.05930.3178-15.3085-18.1579-29.6545
43.4059-0.3710.86412.02340.01693.2472-0.02080.02540.0420.04590.03340.28860.0704-0.2085-0.01050.1809-0.04540.02210.1702-0.00670.2257-16.3574-33.804-21.3235
52.25860.5701-0.81282.2833-0.34972.64430.1063-0.23510.11610.4906-0.03410.1562-0.10690.0551-0.05070.2411-0.0060.02990.2083-0.02640.1505-4.6444-30.1865-8.0329
61.7037-0.1238-0.31313.586-0.1041.52190.1461-0.21320.2530.4357-0.04660.0979-0.21690.2145-0.10290.2375-0.08790.03140.2421-0.05340.21132.3939-15.8381-12.9386
76.67962.87853.53652.82911.84513.1558-0.17620.4450.2208-0.01990.2103-0.0518-0.05330.50740.0420.1824-0.02370.02560.3258-0.01290.15156.9345-26.5182-28.5846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3:36)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 37:79)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 80:142)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 143:209)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 210:288)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 289:348)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 349:392)

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