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- PDB-2gzf: Crystal structure of the E9 DNase domain with a mutant immunity p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gzf | ||||||
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Title | Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y54F) | ||||||
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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. / Kleanthous, C. / Hemmings, A.M. | ||||||
![]() | ![]() Title: Crystal Structure of the Complex of the Colicin E9 DNase Domain with a Mutant Immunity Protein, IM9 (Y54F) Authors: Kuhlmann, U.C. / Santi, P.S. / Kolade, O.O. / 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 | ![]() | 65.1 KB | Display | ![]() |
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PDB format | ![]() | 46.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Unit cell |
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Details | The crystallographic asymmetric unit contains a single copy of the biological unit. |
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Components
#1: Protein | Mass: 9576.500 Da / Num. of mol.: 1 / Mutation: Y54F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 15120.021 Da / Num. of mol.: 1 / Fragment: Colicin E9,C-terminal Domain,DNase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffussion, sitting drop / pH: 5.3 Details: 24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOUR DIFFUSSION,SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 7, 1999 |
Radiation | Monochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 20738 / Num. obs: 20738 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.042 / Χ2: 2.279 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.23 / Num. unique all: 2037 / Χ2: 1.937 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1EMV Resolution: 1.75→19.41 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.637 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.127 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.194 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→19.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 Å / Total num. of bins used: 20
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