+Open data
-Basic information
Entry | Database: PDB / ID: 4id6 | ||||||
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Title | Crystal Structure of Staphylococcal nuclease mutant V23I/I72L | ||||||
Components | ThermonucleaseMicrococcal nuclease | ||||||
Keywords | HYDROLASE | ||||||
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 / Resolution: 1.898 Å | ||||||
Authors | Hansen, S.W. / Janowska, K. / Stites, W.E. / Sakon, J. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Staphylococcal nuclease mutant V23I/I72L Authors: Hansen, S.W. / Janowska, K. / Stites, W.E. / Sakon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4id6.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4id6.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 4id6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/4id6 ftp://data.pdbj.org/pub/pdb/validation_reports/id/4id6 | HTTPS FTP |
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-Related structure data
Related structure data | 1ey0S 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: 16857.357 Da / Num. of mol.: 1 / Mutation: V23I, I72L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Production host: Escherichia coli (E. coli) / References: UniProt: P00644, micrococcal nuclease |
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#2: 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: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K | |||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 12, 2012 / Details: mirrors | |||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.898→21.62 Å / Num. all: 26211 / Num. obs: 11415 / % possible obs: 98.1 % / Observed criterion σ(F): 50 / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.2 | |||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PBD ENTRY 1EY0 Resolution: 1.898→21.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.222 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 40.175 Å2
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Refinement step | Cycle: LAST / Resolution: 1.898→21.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.898→1.947 Å / Total num. of bins used: 20
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