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Yorodumi- PDB-1yyk: Crystal structure of RNase III from Aquifex Aeolicus complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yyk | ||||||
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Title | Crystal structure of RNase III from Aquifex Aeolicus complexed with double-stranded RNA at 2.5-angstrom resolution | ||||||
Components |
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Keywords | HYDROLASE/RNA / Ribonuclease III / double-stranded RNA / 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: 2.5 Å | ||||||
Authors | Gan, J. / Tropea, J.E. / Austin, B.P. / Court, D.L. / Waugh, D.S. / Ji, X. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Intermediate states of ribonuclease III in complex with double-stranded RNA Authors: Gan, J. / Tropea, J.E. / Austin, B.P. / Court, D.L. / Waugh, D.S. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yyk.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yyk.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 1yyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yyk_validation.pdf.gz | 486.7 KB | Display | wwPDB validaton report |
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Full document | 1yyk_full_validation.pdf.gz | 499.8 KB | Display | |
Data in XML | 1yyk_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 1yyk_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/1yyk ftp://data.pdbj.org/pub/pdb/validation_reports/yy/1yyk | HTTPS FTP |
-Related structure data
Related structure data | 1yyoC 1yywC 1yz9C 1i4sS 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: 3827.336 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: 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 #3: Chemical | ChemComp-TRS / | #4: 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: 2.57 Å3/Da / Density % sol: 55.5 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Magnesium formate, PEG3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||
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: BRUKER PROTEUM 300 / Detector: CCD / Date: Dec 14, 2003 / 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: 2.5→29.08 Å / Num. all: 21859 / Num. obs: 21859 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1.1 / Num. unique all: 2170 / % possible all: 57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1I4S Resolution: 2.5→29.08 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 546018.76 / 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: 23.6993 Å2 / ksol: 0.250825 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
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Xplor file |
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