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Yorodumi- PDB-9c11: Crystal structure of Staphylococcal nuclease variant Delta+PHS L3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9c11 | |||||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS L36R at cryogenic temperature | |||||||||
Components | Nuclease A | |||||||||
Keywords | HYDROLASE / Arginine / Domain-Swapping / 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 / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Zhang, Y. / Schlessman, J.L. / Siegler, M.A. / Garcia-Moreno E., B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Domain-swapping promoted by the introduction of a charge in the hydrophobic interior of a protein Authors: Zhang, Y. / Schlessman, J.L. / Robinson, A.C. / Garcia-Moreno E., B. / Khangulov, V.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c11.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c11.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 9c11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/9c11 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/9c11 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 16187.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pET24a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00644 #2: Chemical | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | 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: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 28% MPD 25mM K Phosphate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 14, 2023 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→23.21 Å / Num. obs: 22934 / % possible obs: 99.8 % / Redundancy: 9.6 % / Biso Wilson estimate: 25.76 Å2 / Rmerge(I) obs: 0.015 / Rsym value: 0.043 / Net I/σ(I): 104.39 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.88 / Num. unique obs: 2297 / Rsym value: 0.242 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→21.76 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.143 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.172 / 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: 43.065 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→21.76 Å
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