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Yorodumi- PDB-1jfz: Crystal Structure of MN(II)-Complex of RNAse III Endonuclease Dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jfz | ||||||
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Title | Crystal Structure of MN(II)-Complex of RNAse III Endonuclease Domain from Aquifex Aeolicus at 2.10 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: 2.1 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 | 1jfz.cif.gz | 153.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jfz.ent.gz | 117.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/1jfz ftp://data.pdbj.org/pub/pdb/validation_reports/jf/1jfz | HTTPS FTP |
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-Related structure data
Related structure data | 1i4sSC 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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Details | The biological assembly is a dimer. The asymmetric unit is composed from two independent dimers: first dimer is composed from identical chains A and B, and second dimer from identical chains C and D |
-Components
#1: Protein | Mass: 18163.012 Da / Num. of mol.: 4 / Fragment: N-TERMINAL ENDONUCLEASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / 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-MN / #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: 2.13 Å3/Da / Density % sol: 39.7 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18-20 ℃ / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.045 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 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: 2.1→30 Å / Num. all: 33591 / Num. obs: 33591 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.165 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.3132 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.023 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 2.985 / Num. unique all: 2721 / % possible all: 74.7 |
Reflection | *PLUS Num. measured all: 72740 |
Reflection shell | *PLUS % possible obs: 74.7 % / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1I4S Resolution: 2.1→30 Å / Num. parameters: 21898 / Num. restraintsaints: 20454 / 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: 31.865 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.228 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5640 | ||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 4 / Rfactor all: 0.209 / Rfactor obs: 0.191 / Rfactor Rfree: 0.277 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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