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Yorodumi- PDB-8qjp: SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qjp | |||||||||||||||
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Title | SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with uridine - 5'- monophosphate | |||||||||||||||
Components | S1/P1 Nuclease | |||||||||||||||
Keywords | HYDROLASE / Nuclease | |||||||||||||||
Function / homology | PHOSPHATE ION / URIDINE-5'-MONOPHOSPHATE / : Function and homology information | |||||||||||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 | 8qjp.cif.gz | 231.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qjp.ent.gz | 177.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qjp_validation.pdf.gz | 5.3 MB | Display | wwPDB validaton report |
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Full document | 8qjp_full_validation.pdf.gz | 5.4 MB | Display | |
Data in XML | 8qjp_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 8qjp_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/8qjp ftp://data.pdbj.org/pub/pdb/validation_reports/qj/8qjp | HTTPS FTP |
-Related structure data
Related structure data | 8qjlC 8qjmC 8qjnC 8qjoC 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, 739 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Chemical | #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: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 30 % w/v PEG 8000, 0.2 M Lithium sulfate. Protein concentration 11.8 mg/ml. Cryo-protection by glycerol 20 % v/v. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→43.41 Å / Num. obs: 155893 / % possible obs: 97 % / Redundancy: 5.1 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.09 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7417 / CC1/2: 0.579 / Rrim(I) all: 1.352 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→43.41 Å / Cor.coef. Fo:Fc: 0.979 / SU B: 1.351 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.034 Details: Hydrogens have been added in their riding positions. Data were corrected for lattice translocation defect by applying approach as in doi: 10.1107/S2059798322008397. Last refinement cycle was ...Details: Hydrogens have been added in their riding positions. Data were corrected for lattice translocation defect by applying approach as in doi: 10.1107/S2059798322008397. 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: 20.454 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→43.41 Å
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Refine LS restraints |
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LS refinement shell |
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