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Yorodumi- PDB-2nug: Crystal structure of RNase III from Aquifex aeolicus complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nug | ||||||
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Title | Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 1.7-Angstrom Resolution | ||||||
Components |
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Keywords | hydrolase/RNA / Ribonuclease III / dsRNA / RNA interference / endonucleolytic cleavage / hydrolase-RNA COMPLEX | ||||||
Function / homology | Function and homology information ribonuclease III / ribonuclease III activity / tRNA processing / RNA processing / mRNA processing / rRNA processing / double-stranded RNA binding / regulation of gene expression / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Gan, J.H. / Shaw, G. / Tropea, J.E. / Waugh, D.S. / Court, D.L. / Ji, X. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2007 Title: A stepwise model for double-stranded RNA processing by ribonuclease III. Authors: Gan, J. / Shaw, G. / Tropea, J.E. / Waugh, D.S. / Court, D.L. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nug.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nug.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 2nug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/2nug ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nug | HTTPS FTP |
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-Related structure data
Related structure data | 2nueC 2nufC 1rc7S 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: RNA chain | Mass: 3507.138 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: RNA chain | Mass: 3499.114 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 26147.381 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rnc / Plasmid: pHPK1409 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: O67082, ribonuclease III #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.57 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M MgCl2 + 3.4 M 1,6 Hexanediol in 0.1 M Tris-Cl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 3, 2006 / Details: mirror |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 67288 / Num. obs: 67288 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4607 / % possible all: 62.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RC7 Resolution: 1.7→29.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 174215.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.6616 Å2 / ksol: 0.407442 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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