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Yorodumi- PDB-8qjm: SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qjm | |||||||||||||||
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Title | SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with cytidine-5'-monophosphate | |||||||||||||||
Components | S1/P1 Nuclease | |||||||||||||||
Keywords | HYDROLASE / Nuclease | |||||||||||||||
Function / homology | CYTIDINE-5'-MONOPHOSPHATE / : Function and homology information | |||||||||||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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 | 8qjm.cif.gz | 135.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qjm.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 8qjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qjm_validation.pdf.gz | 4.7 MB | Display | wwPDB validaton report |
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Full document | 8qjm_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 8qjm_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 8qjm_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/8qjm ftp://data.pdbj.org/pub/pdb/validation_reports/qj/8qjm | HTTPS FTP |
-Related structure data
Related structure data | 8qjlC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28354.814 Da / Num. of mol.: 2 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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-Non-polymers , 6 types, 562 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-1PE / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.2 Å3/Da / Density % sol: 44.12 % |
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Crystal grow | Temperature: 291 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 PEG400 30 % 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 21, 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: 1.65→41.66 Å / Num. obs: 57878 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.961 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.149 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.596 / Num. unique obs: 2787 / CC1/2: 0.559 / Rrim(I) all: 0.722 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→41.66 Å / Cor.coef. Fo:Fc: 0.951 / SU B: 1.689 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.099 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: 12.199 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→41.66 Å
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Refine LS restraints |
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LS refinement shell |
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