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Yorodumi- PDB-4g25: Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. tha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g25 | ||||||
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Title | Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana, SeMet substituted form with Sr | ||||||
Components | Pentatricopeptide repeat-containing protein At2g32230, mitochondrial | ||||||
Keywords | RNA BINDING PROTEIN / Metallonuclease / PRORP / Ribonuclease / PIN / tRNA processing / Rnase P / NYN domain / PPR domain / Chloroplasts | ||||||
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 Å | ||||||
Authors | Koutmos, M. / Howard, M.J. / Fierke, C.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing. Authors: Howard, M.J. / Lim, W.H. / 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 | 4g25.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g25.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 4g25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/4g25 ftp://data.pdbj.org/pub/pdb/validation_reports/g2/4g25 | HTTPS FTP |
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-Related structure data
Related structure data | 4g23SC 4g24C 4g26C S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 57317.258 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: At2g32230, F22D22.2 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q66GI4, ribonuclease P |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SR / |
#4: 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: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 18% PEG 3,350, 0.1 M sodium citrate pH 5.5, and 0.02 M SrCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.968 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2012 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: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 45501 / Num. obs: 44773 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rsym value: 0.084 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4456 / Rsym value: 0.63 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4G23 Resolution: 2→33.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.696 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.148 / 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: 44.137 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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