+Open data
-Basic information
Entry | Database: PDB / ID: 7wnu | ||||||
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Title | Mycobacterium tuberculosis Rnase J complex with 7nt RNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information 5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / beta-lactamase activity / beta-lactamase / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Li, J. / Hu, J. / Bao, L. / 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 | 7wnu.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wnu.ent.gz | 175.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/7wnu ftp://data.pdbj.org/pub/pdb/validation_reports/wn/7wnu | HTTPS FTP |
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-Related structure data
Related structure data | 7wntC 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
#1: Protein | Mass: 59601.332 Da / Num. of mol.: 2 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, beta-lactamase #2: RNA chain | Mass: 2259.483 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / Has ligand of interest | N | |
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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: 2.6 Å3/Da / Density % sol: 52.65 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→42.88 Å / Num. obs: 21660 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 59.25 Å2 / Rmerge(I) obs: 0.0405 / Net I/σ(I): 16.77 |
Reflection shell | Resolution: 3.2→3.314 Å / Rmerge(I) obs: 0.156 / Num. unique obs: 2157 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZQ4 Resolution: 3.2→42.88 Å / SU ML: 0.3647 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9492 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 63.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→42.88 Å
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Refine LS restraints |
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LS refinement shell |
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