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Yorodumi- PDB-9cij: Crystal structure of Staphylococcal nuclease variant Delta+PHS V2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cij | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS V23E/L36R at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / ARGININE / ION-PAIR / STAPHYLOCOCCAL NUCLEASE | ||||||
Function / homology | Function and homology information endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zhang, Y. / Schlessman, L.J. / Siegler, M.A. / Garcia-Moreno E., B. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS V23E/L36R at cryogenic temperature Authors: Zhang, Y. / Schlessman, L.J. / Robinson, A.C. / Garcia-Moreno E., B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cij.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cij.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 9cij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cij_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 9cij_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 9cij_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 9cij_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/9cij ftp://data.pdbj.org/pub/pdb/validation_reports/ci/9cij | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16217.484 Da / Num. of mol.: 1 / Mutation: V23E, L36R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: nuc, SACOL0860 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HHM4, micrococcal nuclease |
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#2: Chemical | ChemComp-THP / |
#3: Chemical | ChemComp-CA / |
#4: 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: 2.21 Å3/Da / Density % sol: 44.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 35% MPD, 25mM Potassium Phosphate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5418 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 20, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24.9 Å / Num. obs: 11216 / % possible obs: 99.9 % / Redundancy: 10 % / Rmerge(I) obs: 0.022 / Rsym value: 0.05 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 5.04 / Num. unique obs: 1127 / Rsym value: 0.255 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→24.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.668 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.499 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→24.9 Å
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