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Yorodumi- PDB-6bv8: Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bv8 | ||||||
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Title | Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana complexed with Mn after 3-hour soak with juglone | ||||||
Components | Proteinaceous RNase P 1, chloroplastic/mitochondrial | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / metallonuclease / PRORP / ribonuclease / PIN / tRNA processing / RNAse P / NYN domain / PPR domain / chloroplasts / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Karasik, A. / Wu, N. / Fierke, C.A. / Koutmos, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bv8.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bv8.ent.gz | 153.8 KB | Display | PDB format |
PDBx/mmJSON format | 6bv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bv8_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 6bv8_full_validation.pdf.gz | 449.5 KB | Display | |
Data in XML | 6bv8_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 6bv8_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/6bv8 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/6bv8 | HTTPS FTP |
-Related structure data
Related structure data | 6bv5C 6bv6C 6bv9C 4g23S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#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.) Arabidopsis thaliana (thale cress) / Gene: PRORP1, At2g32230, F22D22.2 / Plasmid: Plasmid / Details (production host): pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta (DE3) / References: UniProt: Q66GI4, ribonuclease P |
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-Non-polymers , 5 types, 241 molecules
#2: Chemical | ChemComp-JUG / | ||
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#3: Chemical | ChemComp-MN / | ||
#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.08 % |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 9, 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: 1.0331 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→86.99 Å / Num. obs: 38500 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.6 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4G23 Resolution: 2.1→86.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.741 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.168 / 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: 54.091 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→86.99 Å
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Refine LS restraints |
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