+Open data
-Basic information
Entry | Database: PDB / ID: 7wnt | ||||||
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Title | RNase J from Mycobacterium tuberculosis | ||||||
Components | Ribonuclease J | ||||||
Keywords | RNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information 5'-3' RNA exonuclease activity / RNA endonuclease activity / beta-lactamase / beta-lactamase activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Li, J. / Bao, L. / Hu, J. / Zhan, B. / Li, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structural ans functional study of RNase J from Mycobacterium tuberculosis Authors: Li, J. / Hu, J. / Bao, L. / Zhan, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wnt.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wnt.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/7wnt ftp://data.pdbj.org/pub/pdb/validation_reports/wn/7wnt | HTTPS FTP |
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-Related structure data
Related structure data | 7wnuC 3zq4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 59601.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: rnj / Production host: Escherichia coli (E. coli) References: UniProt: P9WGZ9, Hydrolases; Acting on ester bonds, beta-lactamase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.63 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES (pH 7.5) 4.3 M NaCl |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→47.64 Å / Num. obs: 33845 / % possible obs: 99.65 % / Redundancy: 2 % / Biso Wilson estimate: 58.61 Å2 / Rmerge(I) obs: 0.01581 / Net I/σ(I): 22.93 |
Reflection shell | Resolution: 2.44→2.52 Å / Rmerge(I) obs: 0.2589 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 3269 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZQ4 Resolution: 2.44→47.64 Å / SU ML: 0.3608 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3153 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→47.64 Å
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Refine LS restraints |
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LS refinement shell |
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