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- PDB-6bv9: Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana af... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bv9 | ||||||
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Title | Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana after overnight soak with juglone | ||||||
![]() | Proteinaceous RNase P 1, chloroplastic/mitochondrial | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / metallonuclease / PRORP / ribonuclease / PIN / tRNA processing / RNAse P / NYN domain / PPR domain / chloroplasts / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / chloroplast / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karasik, A. / Wu, N. / Fierke, C.A. / Koutmos, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibition of protein-only RNase P with Gambogic acid and Juglone Authors: Wu, N. / Karasik, A. / Muehlbauer, L. / Koutmos, M. / Fierke, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.8 KB | Display | ![]() |
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PDB format | ![]() | 153 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.2 KB | Display | ![]() |
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Full document | ![]() | 457.8 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bv5C ![]() 6bv6C ![]() 6bv8C ![]() 4g23S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56660.734 Da / Num. of mol.: 1 / Fragment: UNP residues 77-572 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 18% PEG3350, 0.1 M sodium citrate tribasic, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2017 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→87.21 Å / Num. obs: 39128 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4G23 Resolution: 2.1→87.21 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.85 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.17 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→87.21 Å
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Refine LS restraints |
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