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Open data
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Basic information
Entry | Database: PDB / ID: 2vlq | ||||||
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Title | F86A mutant of E9 DNase domain in complex with Im9 | ||||||
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![]() | PROTEIN BINDING / PROTEIN-BINDING / PROTEIN-PROTEIN INTERACTION / METAL-BINDING / ANTIMICROBIAL / BACTERIOCIN IMMUNITY / HYDROLASE / ANTIBIOTIC / BACTERIOCIN / ENDONUCLEASE / ZINC / COLICIN / PLASMID / NUCLEASE / HTH MOTIF | ||||||
Function / homology | ![]() extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / protein domain specific binding / protein-containing complex / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Keeble, A.H. / Joachimiak, L.A. / Mate, M.J. / Meenan, N. / Kirkpatrick, N. / Baker, D. / Kleanthous, C. | ||||||
![]() | ![]() Title: Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases. Authors: Keeble, A.H. / Joachimiak, L.A. / Mate, M.J. / Meenan, N. / Kirkpatrick, N. / Baker, D. / Kleanthous, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.7 KB | Display | ![]() |
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PDB format | ![]() | 47 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455 KB | Display | ![]() |
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Full document | ![]() | 458.6 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vlnC ![]() 2vloC ![]() 2vlpC ![]() 1emvS C: citing same article ( 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: 9592.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 15043.924 Da / Num. of mol.: 1 / Fragment: DNASE DOMAIN, RESIDUES 450-582 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P09883, Hydrolases; Acting on ester bonds | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | RESIDUE PHE86 MUTATED TO ALA | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47.4 % / Description: NONE |
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Crystal grow | Details: 2.9 M AMMONIUM SULPHATE AND 100 MM BIS-TRIS PH 5.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→41.17 Å / Num. obs: 29183 / % possible obs: 97.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.1 / % possible all: 85.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EMV Resolution: 1.6→41.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.523 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.089 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→41.17 Å
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Refine LS restraints |
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