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Yorodumi- PDB-7tuv: Crystal structure of the exoribonucleolytic module of T. brucei RRP44 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tuv | ||||||||||||
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Title | Crystal structure of the exoribonucleolytic module of T. brucei RRP44 | ||||||||||||
Components |
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Keywords | HYDROLASE/RNA / ribonuclease / RNaseII family / HYDROLASE / HYDROLASE-RNA complex | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Trypanosoma brucei (eukaryote) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.225 Å | ||||||||||||
Authors | Cesaro, G. / Guimaraes, B.G. | ||||||||||||
Funding support | Brazil, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Trypanosoma brucei RRP44: a versatile enzyme for processing structured and non-structured RNA substrates. Authors: Cesaro, G. / da Soler, H.T. / Guerra-Slompo, E.P. / Haouz, A. / Legrand, P. / Zanchin, N.I.T. / Guimaraes, B.G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tuv.cif.gz | 289.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tuv.ent.gz | 229.8 KB | Display | PDB format |
PDBx/mmJSON format | 7tuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tuv_validation.pdf.gz | 838.5 KB | Display | wwPDB validaton report |
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Full document | 7tuv_full_validation.pdf.gz | 845.9 KB | Display | |
Data in XML | 7tuv_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 7tuv_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/7tuv ftp://data.pdbj.org/pub/pdb/validation_reports/tu/7tuv | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 84359.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: RRP44 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95Z12 | ||||
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#2: RNA chain | Mass: 1257.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | ChemComp-U5P / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 15% (w/v) PEG 20000, 0.1 M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.225→77.632 Å / Num. obs: 24678 / % possible obs: 93.8 % / Redundancy: 24 % / CC1/2: 0.998 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.225→2.554 Å / Num. unique obs: 1235 / CC1/2: 0.632 / % possible all: 70.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: homology model Resolution: 2.225→77.63 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.865 / SU R Cruickshank DPI: 0.91 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.264 / SU Rfree Blow DPI: 0.345 / SU Rfree Cruickshank DPI: 0.344
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Displacement parameters | Biso mean: 49.61 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.225→77.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.43 Å
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Refinement TLS params. | Origin x: 29.5012 Å / Origin y: -9.2357 Å / Origin z: 21.9302 Å
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Refinement TLS group | Selection details: { A|* } |