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Yorodumi- PDB-6xse: Crystal structure of Staphylococcal nuclease variant Delta+PHS F3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xse | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS F34Y at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / nuclease / polar group / pdTp | ||||||
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: 2.1 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 F34Y 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 | 6xse.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xse.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xse_validation.pdf.gz | 795.1 KB | Display | wwPDB validaton report |
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Full document | 6xse_full_validation.pdf.gz | 795.5 KB | Display | |
Data in XML | 6xse_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 6xse_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/6xse ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xse | 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: 16159.463 Da / Num. of mol.: 1 / Fragment: UNP residues 83-231 / Mutation: F34Y/G50F/V51N/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: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 26% 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 16, 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: 2.1→38 Å / Num. obs: 8368 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.021 / Net I/σ(I): 41.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 5.77 / Num. unique obs: 844 / % 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: 2.1→24.63 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2342 / WRfactor Rwork: 0.1986 / FOM work R set: 0.7041 / SU B: 9.209 / SU ML: 0.229 / SU R Cruickshank DPI: 0.2706 / SU Rfree: 0.2205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.4 Å2 / Biso mean: 32.973 Å2 / Biso min: 17.14 Å2
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Refinement step | Cycle: final / Resolution: 2.1→24.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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