+Open data
-Basic information
Entry | Database: PDB / ID: 6t4r | ||||||
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Title | Crystal structure of Trypanosoma brucei Morn1 | ||||||
Components | MORN repeat-containing protein 1 | ||||||
Keywords | STRUCTURAL PROTEIN / MORN repeat / MORN1 / Trypanosoma | ||||||
Function / homology | bilobe structure / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / endocytosis / MORN repeat-containing protein 1 Function and homology information | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.352 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 | 6t4r.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t4r.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6t4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/6t4r ftp://data.pdbj.org/pub/pdb/validation_reports/t4/6t4r | HTTPS FTP |
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-Related structure data
Related structure data | 6t4dSC 6t68C 6t69C 6t6qC 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: 24630.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb927.6.4670 / Production host: Escherichia coli (E. coli) / References: UniProt: Q587D3 #2: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 43.33 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.166 M Tris-HCl pH 8.8, 0.15 M MgCl2, 0.45 M KI, 24% PEG 2000 MME, and 4% glycerol PH range: 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→48.28 Å / Num. obs: 17460 / % possible obs: 95.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1247 / CC1/2: 0.897 / Rpim(I) all: 0.25 / Rrim(I) all: 0.532 / % possible all: 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6T4D Resolution: 2.352→48.28 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: FREE R-VALUE / ESU R: 0.606 / ESU R Free: 0.288 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: 35.095 Å2
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Refinement step | Cycle: LAST / Resolution: 2.352→48.28 Å
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Refine LS restraints |
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LS refinement shell |
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