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Yorodumi- PDB-4m30: Crystal structure of RNASE III complexed with double-stranded RNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m30 | ||||||
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Title | Crystal structure of RNASE III complexed with double-stranded RNA AND AMP (TYPE II CLEAVAGE) | ||||||
Components |
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Keywords | HYDROLASE/RNA / RNase III / hydrolase / dsRNA / RNA binding / RNA processing / 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: 2.501 Å | ||||||
Authors | Gan, J. / Liang, Y.-H. / Shaw, G.X. / Tropea, J.E. / Waugh, D.S. / Ji, X. | ||||||
Citation | Journal: Annu. Rev. Genet. / Year: 2013 Title: RNase III: Genetics and Function; Structure and Mechanism. Authors: Court, D.L. / Gan, J. / Liang, Y.H. / Shaw, G.X. / Tropea, J.E. / Costantino, N. / 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 | 4m30.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m30.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 4m30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/4m30 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/4m30 | HTTPS FTP |
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-Related structure data
Related structure data | 4m2zC 1rc7S C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein / RNA chain , 2 types, 4 molecules ABCD
#1: Protein | Mass: 26147.381 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_946, rnc / Plasmid: pHPK1409 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: O67082, ribonuclease III #2: RNA chain | Mass: 8651.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Cleavage product of a R1.1 RNA derivative |
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-Non-polymers , 4 types, 82 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-MPD / ( | #5: Chemical | #6: 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: 3.06 Å3/Da / Density % sol: 59.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 70% (v/v) MPD in 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2006 / Details: mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→30 Å / Num. all: 28418 / Num. obs: 28418 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 74.45 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.003 / Net I/σ(I): 18.569 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RC7 Resolution: 2.501→29.116 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 25.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.936 Å2 / ksol: 0.364 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.78 Å2 / Biso mean: 80.2303 Å2 / Biso min: 46.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.501→29.116 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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