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Yorodumi- PDB-3hej: Crystal structure of Staphylococcal nuclease variant Delta+PHS T6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hej | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS T62R at cryogenic temperature | ||||||
Components | ThermonucleaseMicrococcal nuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / domain swapping / arginine / Calcium / Endonuclease / Membrane / Metal-binding / Nuclease / Secreted / Zymogen | ||||||
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: 1.8 Å | ||||||
Authors | Khangulov, V.S. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno, E.B. | ||||||
Citation | Journal: To be Published Title: Domain swapping promoted by a single mutation that introduces an ionizable group into the hydrophobic core of a protein Authors: Khangulov, V.S. / Schlessman, J.L. / Heroux, A. / 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 | 3hej.cif.gz | 136.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hej.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/3hej ftp://data.pdbj.org/pub/pdb/validation_reports/he/3hej | HTTPS FTP |
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-Related structure data
Related structure data | 3owfC 3heh 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ADBC
#1: Protein | Mass: 16199.555 Da / Num. of mol.: 4 / Mutation: G50F, V51N, T62R, 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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease |
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-Non-polymers , 5 types, 486 molecules
#2: Chemical | ChemComp-THP / #3: Chemical | ChemComp-MPD / ( | #4: Chemical | #5: Chemical | ChemComp-MRD / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 24% MPD, 25 mM Potassium Phosphate, Calcium Chloride, 5% Glycerol, 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: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2008 Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes |
Radiation | Monochromator: Double silicon(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→68.04 Å / Num. all: 62888 / Num. obs: 62385 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.046 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 99.4 |
-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 / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.825 / SU B: 2.851 / SU ML: 0.089 / SU R Cruickshank DPI: 0.135 / SU Rfree: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 72.81 Å2 / Biso mean: 26.557 Å2 / Biso min: 7.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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