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Yorodumi- PDB-4oe1: Crystal structure of the pentatricopeptide repeat protein PPR10 (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oe1 | ||||||
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Title | Crystal structure of the pentatricopeptide repeat protein PPR10 (C256S/C430S/C449S) in complex with an 18-nt PSAJ rna element | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / PENTATRICOPEPTIDE REPEATS / SUPERHELICAL / RNA BINDING PROTEIN / RNA / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information mRNA stabilization / chloroplast stroma / mRNA processing / mRNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Li, Q. / Yan, C. / Wu, J. / Yin, P. / Yan, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Examination of the dimerization states of the single-stranded RNA recognition protein pentatricopeptide repeat 10 (PPR10). Authors: Li, Q. / Yan, C. / Xu, H. / Wang, Z. / Long, J. / Li, W. / Wu, J. / Yin, P. / Yan, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oe1.cif.gz | 553.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oe1.ent.gz | 458.9 KB | Display | PDB format |
PDBx/mmJSON format | 4oe1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/4oe1 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/4oe1 | HTTPS FTP |
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-Related structure data
Related structure data | 4m59S 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
#1: Protein | Mass: 79301.672 Da / Num. of mol.: 2 / Fragment: UNP residues 69-786 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: ppr10, ZEAMMB73_867042 / Production host: Escherichia coli (E. coli) / References: UniProt: B8Y6I0 #2: RNA chain | Mass: 5595.259 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-PO4 / | |
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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: 2.3 Å3/Da / Density % sol: 46.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 9% PEG 3350, 0.1M MES 5.5, 6% Tacsimate, pH 6.0, 70 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2013 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. all: 37816 / Num. obs: 37060 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M59 Resolution: 2.8→34.259 Å / SU ML: 0.5 / σ(F): 1.35 / Phase error: 31.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.44 Å2 / ksol: 0.307 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→34.259 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 95.3906 Å / Origin y: 40.5851 Å / Origin z: -8.9344 Å
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Refinement TLS group | Selection details: all |