+Open data
-Basic information
Entry | Database: PDB / ID: 6e4o | ||||||
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Title | Structure of apo T. brucei RRM: P4(1)2(1)2 form | ||||||
Components | RNA-binding protein, putative | ||||||
Keywords | RNA BINDING PROTEIN / RRM / 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: 1.8 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 | 6e4o.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e4o.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 6e4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/6e4o ftp://data.pdbj.org/pub/pdb/validation_reports/e4/6e4o | HTTPS FTP |
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-Related structure data
Related structure data | 6e4nSC 6e4pC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7798.736 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q389P7 #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: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.2-1.4 M trisodium citrate, HEPES buffer |
-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 24, 2010 |
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→38.676 Å / Num. obs: 28420 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / CC1/2: 0.997 / Rpim(I) all: 0.035 / Rsym value: 0.05 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.8→1.97 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.3 / CC1/2: 0.977 / Rpim(I) all: 0.208 / Rsym value: 0.212 / % possible all: 80.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6E4N Resolution: 1.8→38.676 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.34
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 40.113 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.64 Å2 / Biso mean: 23.49 Å2 / Biso min: 6.07 Å2
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Refinement step | Cycle: final / Resolution: 1.8→38.676 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: 10
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Refinement TLS params. | Method: refined / Origin x: 23.5625 Å / Origin y: -4.4708 Å / Origin z: -0.5355 Å
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Refinement TLS group |
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