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Yorodumi- PDB-3u9o: Crystal structure of Staphylococcal nuclease variant NVIAGA/N100G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u9o | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant NVIAGA/N100G at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / hyperstable variant | ||||||
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: 1.95 Å | ||||||
Authors | Schlessman, J.L. / Doctrow, B.M. / Garcia-Moreno E., B. | ||||||
Citation | Journal: To be Published Title: Local flexibility as a determinant of pKa values of surface ionizable groups in proteins Authors: Baran, K.L. / Doctrow, B.M. / Chimenti, M. / Herbst, K. / Fitch, C.A. / Majumdar, A. / 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 | 3u9o.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u9o.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 3u9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u9o_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 3u9o_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 3u9o_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 3u9o_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/3u9o ftp://data.pdbj.org/pub/pdb/validation_reports/u9/3u9o | HTTPS FTP |
-Related structure data
Related structure data | 4e6iC 4evoC 2rdfS S: Starting model for refinement C: citing same article (ref.) |
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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: 16723.312 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: D21N/T33V/T41I/S59A/N100G/P117G/S128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 40% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Aug 15, 2011 / Details: multi-layer optics |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 10952 / Num. obs: 10952 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.81 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.0208 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 15.83 % / Rmerge(I) obs: 0.2851 / Mean I/σ(I) obs: 3.28 / Num. unique all: 1509 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 35.61 / 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 2RDF Resolution: 1.95→30.34 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2233 / WRfactor Rwork: 0.1754 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7925 / SU B: 9.45 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1752 / SU Rfree: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.24 Å2 / Biso mean: 35.9681 Å2 / Biso min: 17.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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