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- PDB-1rc5: CRYSTAL STRUCTURE OF MG(II)-COMPLEX OF RNASE III ENDONUCLEASE DOM... -
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Open data
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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 | ||||||
![]() | Ribonuclease III | ||||||
![]() | HYDROLASE / RIBONUCLEASE / RNASE III / DOUBLE-STRANDED RNA / RNA INTERFERENCE / ENDONUCLEASE DOMAIN / ENDONUCLEOLYTIC CLEAVAGE | ||||||
Function / homology | ![]() ribonuclease III / deoxyribonuclease I activity / ribonuclease III activity / pre-miRNA processing / siRNA processing / RISC complex / tRNA processing / RNA processing / mRNA processing / rRNA processing ...ribonuclease III / deoxyribonuclease I activity / ribonuclease III activity / pre-miRNA processing / siRNA processing / RISC complex / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blaszczyk, J. / Gan, J. / Ji, X. | ||||||
![]() | ![]() 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: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152 KB | Display | ![]() |
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PDB format | ![]() | 116.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 461.8 KB | Display | ![]() |
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Full document | ![]() | 495.9 KB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 50.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rc7C ![]() 1i4sS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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