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Yorodumi- PDB-3d4w: Crystal structure of Staphylococcal nuclease variant Delta+PHS A1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d4w | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS A109R at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / hyperstable variant / internal arg / Endonuclease / Metal-binding / 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 / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Harms, M.J. / Schlessman, J.L. / Garcia-Moreno, E.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Arginine residues at internal positions in a protein are always charged. Authors: Harms, M.J. / Schlessman, J.L. / Sue, G.R. / 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 | 3d4w.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d4w.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 3d4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d4w_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 3d4w_full_validation.pdf.gz | 439.8 KB | Display | |
Data in XML | 3d4w_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 3d4w_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/3d4w ftp://data.pdbj.org/pub/pdb/validation_reports/d4/3d4w | HTTPS FTP |
-Related structure data
Related structure data | 3d8gC 3dhqC 1tqoS C: citing same article (ref.) 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: 16229.580 Da / Num. of mol.: 1 / Fragment: UNP database residues 80-228 / Mutation: G50F, V51N, A109R, 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: Q8NXI6, 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: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 43% 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: Nov 10, 2006 / 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: 1.9→34.1 Å / Num. all: 12416 / Num. obs: 12416 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.05 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.0196 / Rsym value: 0.0394 / Net I/σ(I): 41.54 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.91 % / Rmerge(I) obs: 0.1077 / Mean I/σ(I) obs: 8.46 / Num. unique all: 1692 / Rsym value: 0.188 / % possible all: 98.4 |
-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 Starting model: PDB entry 1tqo, all waters removed, b = 20.0, ILE-92 truncated to ALA Resolution: 1.9→31.3 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.177 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.608 / ESU R Free: 0.162 / Stereochemistry target values: Engh & Huber
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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: 16.382 Å2
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Refine analyze | Luzzati coordinate error obs: 0.221 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→31.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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