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Yorodumi- PDB-6lvr: Crystal structure of the PPR domain of Arabidopsis thaliana prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lvr | ||||||
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Title | Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Protein-only RNase P tRNA processing tRNA complex Pentatricopeptide repeat convergent evolution | ||||||
Function / homology | Function and homology information ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / chloroplast / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Teramoto, T. / Hall, T.M.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA. Authors: Teramoto, T. / Kaitany, K.J. / Kakuta, Y. / Kimura, M. / Fierke, C.A. / Hall, T.M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lvr.cif.gz | 323.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lvr.ent.gz | 253.5 KB | Display | PDB format |
PDBx/mmJSON format | 6lvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/6lvr ftp://data.pdbj.org/pub/pdb/validation_reports/lv/6lvr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23442.951 Da / Num. of mol.: 2 / Mutation: Y266N, F284Q, F291Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRORP1, At2g32230, F22D22.2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66GI4, ribonuclease P #2: RNA chain | Mass: 24890.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) #3: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | Authors Substituted SASS for original EAATESSP sequence. | |
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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: 4.48 Å3/Da / Density % sol: 72.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.5 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 42492 / % possible obs: 99.9 % / Redundancy: 5 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.124 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 2074 / CC1/2: 0.792 / CC star: 0.94 / Rpim(I) all: 0.48 / Rrim(I) all: 1.075 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G24, 1EHZ Resolution: 2.85→49.312 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: FREE R-VALUE / ESU R Free: 0.295 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: 120.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→49.312 Å
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Refine LS restraints |
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LS refinement shell |
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