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Yorodumi- PDB-1rc5: CRYSTAL STRUCTURE OF MG(II)-COMPLEX OF RNASE III ENDONUCLEASE DOM... -
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-Basic information
Entry | Database: PDB / ID: 1rc5 | ||||||
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Title | CRYSTAL STRUCTURE OF MG(II)-COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS AT 2.30 ANGSTROM RESOLUTION | ||||||
Components | Ribonuclease III | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / RNASE III / DOUBLE-STRANDED RNA / RNA INTERFERENCE / ENDONUCLEASE DOMAIN / ENDONUCLEOLYTIC CLEAVAGE | ||||||
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: 2.3 Å | ||||||
Authors | Blaszczyk, J. / Gan, J. / Ji, X. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Noncatalytic Assembly of Ribonuclease III with Double-Stranded RNA. Authors: Blaszczyk, J. / Gan, J. / Tropea, J.E. / Court, D.L. / Waugh, D.S. / Ji, X. #1: Journal: Structure / Year: 2001 Title: Crystallographic and Modelling Studies of RNase III Suggest a Mechanism for Double-Stranded RNA Cleavage Authors: Blaszczyk, J. / Tropea, J.E. / Bubunenko, M. / Routzahn, K.M. / Waugh, D.S. / Court, D.L. / Ji, X. | ||||||
History |
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Remark 999 | SEQUENCE EXPRESSED WITH A N-TERMINAL GLYCINE RESIDUE, AND WITH SIX-HISTIDINE-TAGGED C-TERMINUS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rc5.cif.gz | 152 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rc5.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/1rc5 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/1rc5 | HTTPS FTP |
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-Related structure data
Related structure data | 1rc7C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18163.012 Da / Num. of mol.: 4 / Fragment: N-TERMINAL ENDONUCLEASE DOMAIN (RESIDUES 1-147) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: RNC, AQ_946 / Plasmid: PKM803 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67082, ribonuclease III #2: Chemical | ChemComp-MG / #3: 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: 2.08 Å3/Da / Density % sol: 39.5 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, TRIS-HCL, ACETATE, CHLORIDE, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.045 / Wavelength: 1.045 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2001 / Details: MIRROR |
Radiation | Monochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.045 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 24431 / Num. obs: 24431 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.822 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.8929 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.42 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3.903 / Num. unique all: 2407 / % possible all: 87.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1I4S Resolution: 2.3→30 Å / Num. parameters: 20239 / Num. restraintsaints: 20369 / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER Details: LEAST-SQUARES REFINEMENT USING THE KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM. CNS was also used for refinement.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975) 201-228 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.611 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.253 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5599 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell |
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