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Yorodumi- PDB-4k5w: Crystal structure of Staphylococcal nuclease variant V23M/L25F/T6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k5w | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant V23M/L25F/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 in 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 | 4k5w.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k5w.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 4k5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k5w_validation.pdf.gz | 815.6 KB | Display | wwPDB validaton report |
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Full document | 4k5w_full_validation.pdf.gz | 817 KB | Display | |
Data in XML | 4k5w_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 4k5w_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/4k5w ftp://data.pdbj.org/pub/pdb/validation_reports/k5/4k5w | HTTPS FTP |
-Related structure data
Related structure data | 3v2tC 4df7C 4dfaC 4dgzC 4du9C 4f7xC 4f8mC 4kd3C 4kd4C 4nklC 4np5C 4odgC 4qf4C 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: 16955.480 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: V23M,L25F,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, 100 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-THP / |
#4: Chemical | ChemComp-PO4 / |
#5: Chemical | ChemComp-MRD / ( |
#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: 2.1 Å3/Da / Density % sol: 41.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 32% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8.0, 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 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 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. all: 16839 / Num. obs: 16839 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.06 / Χ2: 2.283 / Net I/σ(I): 17.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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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→47.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.2166 / WRfactor Rwork: 0.1888 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8708 / SU B: 3.56 / SU ML: 0.064 / SU R Cruickshank DPI: 0.0975 / SU Rfree: 0.0947 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.79 Å2 / Biso mean: 31.2719 Å2 / Biso min: 14.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→47.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.695 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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