+Open data
-Basic information
Entry | Database: PDB / ID: 8qjl | |||||||||||||||
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Title | SmNuc1 nuclease from Stenotrophomonas maltophilia | |||||||||||||||
Components | S1/P1 Nuclease | |||||||||||||||
Keywords | HYDROLASE / Nuclease | |||||||||||||||
Function / homology | : Function and homology information | |||||||||||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||||||||
Authors | Adamkova, K. / Koval, T. / Kolenko, P. / Dohnalek, J. | |||||||||||||||
Funding support | Czech Republic, European Union, 4items
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Citation | Journal: The FEBS Journal / Year: 2024 Title: Substrate preference, RNA binding and active site versatility of the Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study Authors: Adamkova, K. / Trundova, M. / Koval, T. / Hustakova, B. / Duskova, J. / Skalova, T. / Kolenko, P. / Dohnalek, J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qjl.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qjl.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 8qjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qjl_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8qjl_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8qjl_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 8qjl_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/8qjl ftp://data.pdbj.org/pub/pdb/validation_reports/qj/8qjl | HTTPS FTP |
-Related structure data
Related structure data | 8qjmC 8qjnC 8qjoC 8qjpC 8qjqC 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: 28354.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Sequence type 5, study in PMID: 28894437 Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Strain: SanG_2012 / Gene: A1OC_03585 / Plasmid: pET303/CT-His_SmNuc1 / Details (production host): MalE signal peptide / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J7SYS2 | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % / Description: Long rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Lithium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350. Protein concentration 7.5 mg/ml. Cryo-protection by glycerol 20 % v/v. Temp details: Controlled |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: Excillum MetalJet D2 70 kV / Wavelength: 1.3418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Oct 14, 2019 / Details: HELIOS MX, Ga |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→41.22 Å / Num. obs: 50815 / % possible obs: 96 % / Redundancy: 14.3 % / Biso Wilson estimate: 8.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.122 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.166 / Num. unique obs: 2541 / CC1/2: 0.509 / Rrim(I) all: 1.32 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→41.22 Å / Cor.coef. Fo:Fc: 0.978 / SU B: 1.202 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.051 Details: Hydrogens have been added in their riding positions. Last refinement cycle was performed against all reflections.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.934 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→41.22 Å
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Refine LS restraints |
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LS refinement shell |
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