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- PDB-6t6q: Crystal structure of Toxoplasma gondii Morn1 (extended conformation). -

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Basic information

Entry
Database: PDB / ID: 6t6q
TitleCrystal structure of Toxoplasma gondii Morn1 (extended conformation).
ComponentsMembrane occupation and recognition nexus protein MORN1
KeywordsSTRUCTURAL PROTEIN / MORN repeat / MORN1 / Toxoplasma
Function / homologyhistone-lysine N-methyltransferase / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / methyltransferase activity / kinase activity / methylation / metal ion binding / Membrane occupation and recognition nexus protein MORN1
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å
AuthorsGrishkovskaya, I. / Kostan, J. / Sajko, S. / Morriswood, B. / Djinovic-Carugo, K.
CitationJournal: Plos One / Year: 2020
Title: Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats.
Authors: Sajko, S. / Grishkovskaya, I. / Kostan, J. / Graewert, M. / Setiawan, K. / Trubestein, L. / Niedermuller, K. / Gehin, C. / Sponga, A. / Puchinger, M. / Gavin, A.C. / Leonard, T.A. / Svergun, ...Authors: Sajko, S. / Grishkovskaya, I. / Kostan, J. / Graewert, M. / Setiawan, K. / Trubestein, L. / Niedermuller, K. / Gehin, C. / Sponga, A. / Puchinger, M. / Gavin, A.C. / Leonard, T.A. / Svergun, D.I. / Smith, T.K. / Morriswood, B. / Djinovic-Carugo, K.
History
DepositionOct 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Membrane occupation and recognition nexus protein MORN1
BBB: Membrane occupation and recognition nexus protein MORN1


Theoretical massNumber of molelcules
Total (without water)49,4942
Polymers49,4942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-10 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.916, 53.916, 348.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Membrane occupation and recognition nexus protein MORN1 / Phosphatidylinositol-4-phosphate 5-kinase / putative


Mass: 24746.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GPAM tag after 3C cleavage
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50861 / VEG) (eukaryote)
Strain: ATCC 50861 / VEG / Gene: BN1205_094520, TGVEG_310440 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F7VBC6, histone-lysine N-methyltransferase

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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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 8.2, 15% PEG 3350, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.967 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.9→48.92 Å / Num. obs: 12331 / % possible obs: 99.1 % / Redundancy: 8.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.8
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 8 % / Rmerge(I) obs: 2.252 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1819 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T4D

6t4d


Resolution: 2.902→48.92 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.971 / Cross valid method: FREE R-VALUE / ESU R Free: 0.492
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3111 593 4.839 %
Rwork0.2761 --
all0.278 --
obs-12254 98.902 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 86.807 Å2
Baniso -1Baniso -2Baniso -3
1-6.455 Å20 Å20 Å2
2--6.455 Å20 Å2
3----12.911 Å2
Refinement stepCycle: LAST / Resolution: 2.902→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 0 0 3319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133415
X-RAY DIFFRACTIONr_bond_other_d0.0380.0182868
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.6424591
X-RAY DIFFRACTIONr_angle_other_deg2.451.66645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8245414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.27422.83212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08315533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3881518
X-RAY DIFFRACTIONr_chiral_restr0.0380.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024020
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02842
X-RAY DIFFRACTIONr_nbd_refined0.1910.2593
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.22671
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21502
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.21495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.216
X-RAY DIFFRACTIONr_nbd_other0.2430.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0650.22
X-RAY DIFFRACTIONr_mcbond_it1.619.3551662
X-RAY DIFFRACTIONr_mcbond_other1.6099.3541661
X-RAY DIFFRACTIONr_mcangle_it2.75714.0292074
X-RAY DIFFRACTIONr_mcangle_other2.75714.0312075
X-RAY DIFFRACTIONr_scbond_it1.4569.5221753
X-RAY DIFFRACTIONr_scbond_other1.4559.5231754
X-RAY DIFFRACTIONr_scangle_it2.614.2162517
X-RAY DIFFRACTIONr_scangle_other2.59914.2162518
X-RAY DIFFRACTIONr_lrange_it4.439100.2543745
X-RAY DIFFRACTIONr_lrange_other4.438100.2733746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.902-2.9770.52310.493781X-RAY DIFFRACTION90.8277
2.977-3.0590.474390.487782X-RAY DIFFRACTION97.1598
3.059-3.1470.442490.468801X-RAY DIFFRACTION99.4152
3.147-3.2440.517420.414758X-RAY DIFFRACTION99.8752
3.244-3.350.43410.415766X-RAY DIFFRACTION100
3.35-3.4680.374370.35734X-RAY DIFFRACTION100
3.468-3.5990.318460.295709X-RAY DIFFRACTION100
3.599-3.7450.304410.271650X-RAY DIFFRACTION100
3.745-3.9110.334320.233671X-RAY DIFFRACTION99.858
3.911-4.1020.2280.204639X-RAY DIFFRACTION100
4.102-4.3230.24320.214605X-RAY DIFFRACTION99.8433
4.323-4.5850.183340.205572X-RAY DIFFRACTION99.8353
4.585-4.90.227210.204563X-RAY DIFFRACTION99.6587
4.9-5.2920.276250.228507X-RAY DIFFRACTION100
5.292-5.7950.498240.293463X-RAY DIFFRACTION97.4
5.795-6.4750.409230.272439X-RAY DIFFRACTION100
6.475-7.470.319150.259406X-RAY DIFFRACTION100
7.47-9.1320.213100.253355X-RAY DIFFRACTION100
9.132-12.8440.396120.233286X-RAY DIFFRACTION100
12.844-48.920.284110.26174X-RAY DIFFRACTION96.8586

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