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Yorodumi- PDB-3dmu: Crystal structure of Staphylococcal nuclease variant PHS T62K at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dmu | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant PHS T62K at cryogenic temperature | ||||||
Components | ThermonucleaseMicrococcal nuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Khangulov, V.S. / Schlessman, J.L. / Garcia-Moreno, E.B. / Benning, M. / Isom, D. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Staphylococcal nuclease variant PHS T62K at cryogenic temperature Authors: Khangulov, V.S. / Schlessman, J.L. / Isom, D. / 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 | 3dmu.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dmu.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 3dmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/3dmu ftp://data.pdbj.org/pub/pdb/validation_reports/dm/3dmu | HTTPS FTP |
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-Related structure data
Related structure data | 1ey8S 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: 16790.354 Da / Num. of mol.: 1 / Mutation: T62K/P117G/H124L/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: Chemical | ChemComp-MPD / ( |
#4: 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: 2.19 Å3/Da / Density % sol: 43.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 44% MPD, 25 mM Potassium Phosphate, pH 8.0, 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: BRUKER APEX II / Detector: CCD / Date: Jan 20, 2005 / Details: multi-layer optics |
Radiation | Monochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→17.98 Å / Num. all: 14741 / Num. obs: 14710 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.0301 / Rsym value: 0.0199 / Net I/σ(I): 30.16 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.43 % / Rmerge(I) obs: 0.2839 / Mean I/σ(I) obs: 4.05 / Num. unique all: 2016 / Rsym value: 0.2574 / % possible all: 99.3 |
-Phasing
Phasing | Method: molecular replacement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 13486 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EY8.PDB Resolution: 1.8→17 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.133 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.15 / ESU R Free: 0.151 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.909 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→17 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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