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Yorodumi- PDB-1i4s: CRYSTAL STRUCTURE OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i4s | ||||||
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Title | CRYSTAL STRUCTURE OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS AT 2.15 ANGSTROM RESOLUTION | ||||||
Components | RIBONUCLEASE III | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / RNASE III / DOUBLE-STRANDED RNA / CATALYTIC DOMAIN / 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 / MIR / Resolution: 2.15 Å | ||||||
Authors | Blaszczyk, J. / Ji, X. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Crystallographic and modeling 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i4s.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i4s.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/1i4s ftp://data.pdbj.org/pub/pdb/validation_reports/i4/1i4s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17277.078 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ENDONUCLEASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PKM803 / Production host: Escherichia coli (E. coli) / References: UniProt: O67082, ribonuclease III #2: 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: 2.011 Å3/Da / Density % sol: 36.34 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, TRIS-HCL, ACETATE, pH 8.5, 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: 0.98789, 1.01000, 1.03473, 1.04008 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2000 / Details: MIRROR | |||||||||||||||
Radiation | Monochromator: SILICON 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.15→40 Å / Num. all: 16542 / Num. obs: 16542 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.161 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.376 | |||||||||||||||
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.025 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.258 / Num. unique all: 1621 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: NONE Resolution: 2.15→30 Å / Num. parameters: 9323 / Num. restraintsaints: 10091 / 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
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975) 201-228 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.404 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.263 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2696 | ||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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LS refinement shell |
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