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Yorodumi- PDB-6e4n: Structure of the T. brucei TbRGG2 RRM domain: apo R3 crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e4n | ||||||
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Title | Structure of the T. brucei TbRGG2 RRM domain: apo R3 crystal form | ||||||
Components | RNA-binding protein, putative | ||||||
Keywords | RNA BINDING PROTEIN / RRM / TbRGG2 / kRNA editing / RNA binding | ||||||
Function / homology | Function and homology information mitochondrial mRNA processing / mitochondrial mRNA editing complex / cytoplasmic side of mitochondrial outer membrane / kinetoplast / RNA processing / mRNA binding / mitochondrion / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.801 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA. Authors: Travis, B. / Shaw, P.L.R. / Liu, B. / Ravindra, K. / Iliff, H. / Al-Hashimi, H.M. / Schumacher, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e4n.cif.gz | 42.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e4n.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 6e4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/6e4n ftp://data.pdbj.org/pub/pdb/validation_reports/e4/6e4n | HTTPS FTP |
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-Related structure data
Related structure data | 6e4oC 6e4pC 2m8dS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 7816.774 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q389P7 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.4 M citrate, 0.1 M Bis-Tris pH 7 or HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.264 Å / Num. obs: 7045 / % possible obs: 99 % / Redundancy: 1.7 % / CC1/2: 0.994 / Rpim(I) all: 0.04 / Rsym value: 0.07 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.8→1.99 Å / Redundancy: 1.7 % / CC1/2: 0.96 / Rpim(I) all: 0.161 / Rsym value: 0.249 / % possible all: 91.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2M8D Resolution: 1.801→19.264 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.72 Å2 / Biso mean: 17.8 Å2 / Biso min: 3.27 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.801→19.264 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
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Refinement TLS params. | Method: refined / Origin x: -13.8585 Å / Origin y: 2.0009 Å / Origin z: -5.1759 Å
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Refinement TLS group |
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