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Yorodumi- PDB-5diz: Crystal Structure of nuclear proteinaceous RNase P 2 (PRORP2) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5diz | ||||||
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Title | Crystal Structure of nuclear proteinaceous RNase P 2 (PRORP2) from A. thaliana | ||||||
Components | Proteinaceous RNase P 2 | ||||||
Keywords | HYDROLASE / RNA BINDING PROTEIN / Metallonuclease / PRORP / Ribonuclease / tRNA processing / Rnase P / NYN domain / PPR domain / nucleus | ||||||
Function / homology | Function and homology information sno(s)RNA processing / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / mRNA processing / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Karasik, A. / Shanmuganathan, A. / Howard, M.J. / Fierke, C.A. / Koutmos, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5' End Processing Enzymes. Authors: Karasik, A. / Shanmuganathan, A. / Howard, M.J. / Fierke, C.A. / Koutmos, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5diz.cif.gz | 342.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5diz.ent.gz | 286.1 KB | Display | PDB format |
PDBx/mmJSON format | 5diz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5diz_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 5diz_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 5diz_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 5diz_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/5diz ftp://data.pdbj.org/pub/pdb/validation_reports/di/5diz | HTTPS FTP |
-Related structure data
Related structure data | 4g24S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | Monomer by Analytical ultracentrifugation |
-Components
#1: Protein | Mass: 59575.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRORP2, At2g16650, T24I21.6 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q680B9, ribonuclease P #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.6 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 7.8 / Details: 19.9 % (w/v) PEG3000, and 0.21 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2014 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 23244 / % possible obs: 99.1 % / Redundancy: 2 % / Rsym value: 0.059 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.4 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G24 Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 36.722 / SU ML: 0.55 / Cross valid method: THROUGHOUT / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 123.153 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→50 Å
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Refine LS restraints |
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