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Yorodumi- PDB-6t6q: Crystal structure of Toxoplasma gondii Morn1 (extended conformation). -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t6q | ||||||
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Title | Crystal structure of Toxoplasma gondii Morn1 (extended conformation). | ||||||
Components | Membrane occupation and recognition nexus protein MORN1 | ||||||
Keywords | STRUCTURAL PROTEIN / MORN repeat / MORN1 / Toxoplasma | ||||||
Function / homology | histone-lysine N-methyltransferase / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / methyltransferase activity / methylation / kinase activity / phosphorylation / Membrane occupation and recognition nexus protein MORN1 Function and homology information | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å | ||||||
Authors | Grishkovskaya, I. / Kostan, J. / Sajko, S. / Morriswood, B. / Djinovic-Carugo, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t6q.cif.gz | 155.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t6q.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6t6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/6t6q ftp://data.pdbj.org/pub/pdb/validation_reports/t6/6t6q | HTTPS FTP |
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-Related structure data
Related structure data | 6t4dSC 6t4rC 6t68C 6t69C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 8.2, 15% PEG 3350, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.967 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.967 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.807 Å2
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Refinement step | Cycle: LAST / Resolution: 2.902→48.92 Å
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Refine LS restraints |
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LS refinement shell |
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