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Yorodumi- PDB-6xsi: Crystal structure of Staphylococcal nuclease variant Delta+PHS V1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xsi | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS V104T at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / nuclease / hyperstable / pdTp / polar group | ||||||
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 Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Robinson, A.C. / Schlessman, J.L. / 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 V104T at cryogenic temperature Authors: Robinson, A.C. / Schlessman, J.L. / 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 | 6xsi.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xsi.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 6xsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xsi_validation.pdf.gz | 794.6 KB | Display | wwPDB validaton report |
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Full document | 6xsi_full_validation.pdf.gz | 795.2 KB | Display | |
Data in XML | 6xsi_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 6xsi_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/6xsi ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xsi | HTTPS FTP |
-Related structure data
Related structure data | 3bdcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16145.436 Da / Num. of mol.: 1 / Fragment: UNP residues 83-231 / Mutation: G50F/V51N/V104T/P117G/H124L/S128A/Del44-49 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, micrococcal nuclease |
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#2: Chemical | ChemComp-THP / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% MPD, 25 mM potassium phosphate, calcium chloride, THP |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.02 Å / Num. obs: 9632 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.022 / Net I/σ(I): 38.13 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 4.53 / Num. unique obs: 965 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3BDC Resolution: 2→24.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.897 / SU ML: 0.216 / SU R Cruickshank DPI: 0.2272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.189 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.22 Å2 / Biso mean: 40.157 Å2 / Biso min: 20.42 Å2
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Refinement step | Cycle: final / Resolution: 2→24.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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