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- PDB-6w0v: The Crystal Structure of the Mutant Nuclease Domain of Pyocin S8 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w0v | ||||||
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Title | The Crystal Structure of the Mutant Nuclease Domain of Pyocin S8 with its Cognate Immunity Protein | ||||||
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![]() | ANTIMICROBIAL PROTEIN / protein antibiotic / H-H-N DNase / toxin | ||||||
Function / homology | ![]() bacteriocin immunity / cytolysis / toxic substance binding / endonuclease activity / defense response to bacterium / signaling receptor binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Turano, H. / Gomes, F. / Domingos, R.M. / Netto, L.E.S. | ||||||
![]() | ![]() Title: Molecular Structure and Functional Analysis of Pyocin S8 from Pseudomonas aeruginosa Reveals the Essential Requirement of a Glutamate Residue in the H-N-H Motif for DNase Activity. Authors: Turano, H. / Gomes, F. / Domingos, R.M. / Degenhardt, M.F.S. / Oliveira, C.L.P. / Garratt, R.C. / Lincopan, N. / Netto, L.E.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.2 KB | Display | ![]() |
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PDB format | ![]() | 71.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 248.6 KB | Display | ![]() |
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Full document | ![]() | 248.6 KB | Display | |
Data in XML | ![]() | 926 B | Display | |
Data in CIF | ![]() | 3.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uhpS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13782.473 Da / Num. of mol.: 1 / Fragment: Nuclease domain, residues 692-816 / Mutation: E96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 9315.317 Da / Num. of mol.: 1 / Mutation: Y9H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.58 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Sodium Acetate 0.2M, PEG 4000 30%, Tris-HCl 0.1M pH 8.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: flux liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45866 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→30 Å / Num. obs: 37296 / % possible obs: 89.6 % / Redundancy: 9 % / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.012 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.38→1.4 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 648 / CC1/2: 0.795 / Rpim(I) all: 0.296 / % possible all: 32.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UHP Resolution: 1.381→29.983 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.099 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.07 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.364 Å2
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Refinement step | Cycle: LAST / Resolution: 1.381→29.983 Å
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Refine LS restraints |
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LS refinement shell |
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