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Yorodumi- PDB-4oxp: X-ray crystal structure of the S1 and 5'-sensor domains of RNase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oxp | ||||||
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Title | X-ray crystal structure of the S1 and 5'-sensor domains of RNase E from Caulobacter crescentus | ||||||
Components | Ribonuclease E | ||||||
Keywords | HYDROLASE / RNase E / endoribonuclease | ||||||
Function / homology | Function and homology information ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding / magnesium ion binding ...ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding / magnesium ion binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Caulobacter crescentus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Voss, J.E. / Luisi, B.F.L. / Hardwick, S.W. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome. Authors: Voss, J.E. / Luisi, B.F. / Hardwick, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oxp.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oxp.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 4oxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/4oxp ftp://data.pdbj.org/pub/pdb/validation_reports/ox/4oxp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32978.074 Da / Num. of mol.: 1 / Fragment: S1 and 5'-sensor domains (UNP residues 1-270) / Mutation: A172V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: rne, CC_1877 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A749, ribonuclease E |
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#2: 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: 2.31 Å3/Da / Density % sol: 46.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 10% (v/v) Ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9536 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.7 Å / Num. obs: 18069 / % possible obs: 97 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.62 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.8 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→48.7 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.248 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.169 / 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 max: 130.02 Å2 / Biso mean: 55.292 Å2 / Biso min: 23.54 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→48.7 Å
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