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- PDB-2gyk: Crystal structure of the complex of the Colicin E9 DNase domain w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gyk | ||||||
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Title | Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A) | ||||||
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![]() | antibiotic/antibiotic inhibitor / PROTEIN-PROTEIN COMPLEX / 4-HELIX BUNDLE / DNASE DOMAIN / HNH-MOTIF / antibiotic-antibiotic inhibitor COMPLEX | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Santi, P.S. / Kolade, O.O. / Kuhlmann, U.C. / Hemmings, A.M. | ||||||
![]() | ![]() Title: Crystal structures of the complexes of the Colicin E9 DNase domain with mutant immunity proteins Authors: Kuhlmann, U.C. / Santi, P.S. / Kolade, O.O. / Moore, G.R. / James, R. / Kleanthous, C. / Hemmings, A.M. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: Structural and mechanistic basis of immunity towards endonuclease colicins Authors: Kleanthous, C. / Kuhlmann, U.C. / Pommer, A.J. / Ferguson, N. / Radford, S.E. / Moore, G.R. / James, R. / Hemmings, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.8 KB | Display | ![]() |
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PDB format | ![]() | 87.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.2 KB | Display | ![]() |
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Full document | ![]() | 465.6 KB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1emvS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS A DIMER OF THE BIOLOGICAL UNIT |
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Components
#1: Protein | Mass: 9548.490 Da / Num. of mol.: 2 / Mutation: D51A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 15120.021 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, DNASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K Temp details: 277 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2000 |
Radiation | Monochromator: SILICON(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 51260 / Num. obs: 51260 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.027 / Χ2: 1.422 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.045 / Num. unique all: 4468 / Χ2: 0.593 / % possible all: 84.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EMV Resolution: 1.6→19.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.39 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: Engh & Huber / 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: 15.426 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.644 Å / Total num. of bins used: 20
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