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Yorodumi- PDB-4m57: Crystal structure of the pentatricopeptide repeat protein PPR10 f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m57 | ||||||
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Title | Crystal structure of the pentatricopeptide repeat protein PPR10 from maize | ||||||
Components | Chloroplast pentatricopeptide repeat protein 10 | ||||||
Keywords | RNA BINDING PROTEIN / pentatricopeptide repeat / superhelical / RNA | ||||||
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 / SAD / Resolution: 2.86 Å | ||||||
Authors | Yin, P. / Li, Q. / Yan, C. / Liu, Y. / Yan, N. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Authors: Yin, P. / Li, Q. / Yan, C. / Liu, Y. / Liu, J. / Yu, F. / Wang, Z. / Long, J. / He, J. / Wang, H.W. / Wang, J. / Zhu, J.K. / Shi, Y. / Yan, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m57.cif.gz | 270.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m57.ent.gz | 229.1 KB | Display | PDB format |
PDBx/mmJSON format | 4m57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/4m57 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/4m57 | HTTPS FTP |
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-Related 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: 81445.609 Da / Num. of mol.: 1 / Fragment: UNP residues 61-786 / Mutation: C256S, C279S, C430S, C449S 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 |
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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: 2.39 Å3/Da / Density % sol: 48.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8M sodium formate, 0.1M Bis-Tris propane, 0.04M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX325HE / Detector: CCD / Date: Oct 5, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→40 Å / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.85→2.95 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.86→37.08 Å / SU ML: 0.28 / σ(F): 1.37 / Phase error: 26.35 / 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: 54.65 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.86→37.08 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: 0.7092 Å / Origin y: -2.2218 Å / Origin z: 9.2059 Å
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Refinement TLS group | Selection details: all |