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Yorodumi- PDB-4k6d: Crystal structure of Staphylococcal nuclease variant V23M/T62F at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k6d | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant V23M/T62F at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / cavity / pressure | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Caro, J.A. / Flores, E. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno E., B. | ||||||
Citation | Journal: To be Published Title: Pressure effects on proteins Authors: Caro, J.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 | 4k6d.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k6d.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k6d_validation.pdf.gz | 796.8 KB | Display | wwPDB validaton report |
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Full document | 4k6d_full_validation.pdf.gz | 798.4 KB | Display | |
Data in XML | 4k6d_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 4k6d_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/4k6d ftp://data.pdbj.org/pub/pdb/validation_reports/k6/4k6d | HTTPS FTP |
-Related structure data
Related structure data | 4k2kC 4k5xC 1sncS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16921.465 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: V23M,T62F 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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-Non-polymers , 5 types, 85 molecules
#2: Chemical | ChemComp-THP / | ||||
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#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: 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: 2.09 Å3/Da / Density % sol: 41.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 34% 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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2013 Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. all: 20334 / Num. obs: 20334 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.065 / Χ2: 2.235 / Net I/σ(I): 14.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-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 1SNC Resolution: 1.65→47.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2331 / WRfactor Rwork: 0.2089 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8356 / SU B: 2.071 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1033 / SU Rfree: 0.0972 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.103 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 69.4 Å2 / Biso mean: 24.8129 Å2 / Biso min: 10.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→47.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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