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- PDB-1v14: Crystal Structure of the Colicin E9, mutant His103Ala, in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v14 | ||||||
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Title | Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) | ||||||
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![]() | HYDROLASE / HOMING ENDONUCLEASES / COLICIN / HNH MOTIF / BETA-BETA-ALPHA METAL MOTIF | ||||||
Function / homology | ![]() extrachromosomal circular DNA / 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 | ![]() ![]() ![]() | ||||||
![]() | Mate, M.J. / Kleanthous, C. | ||||||
![]() | ![]() Title: Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases Authors: Mate, M.J. / Kleanthous, C. #1: ![]() Title: Specificity in Protein-Protein Interactions: The Structural Basis for Dual Recognition in Endonuclease Colicin-Immunity Protein Complexes Authors: Kuhlmann, U.C. / Pommer, A.J. / Moore, G.M. / James, R. / 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 | ![]() | 145.6 KB | Display | ![]() |
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PDB format | ![]() | 111.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.1 KB | Display | ![]() |
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Full document | ![]() | 472.8 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v13C ![]() 1v15C ![]() 1emvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15052.951 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 450-582 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 2427.605 Da / Num. of mol.: 8 / Source method: obtained synthetically #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE ALA 103 HIS THIS PLASMID-CODED BACTERICIDAL PROTEIN IS AN ENDONUCLEASE ACTIVE ON ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9465 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→70 Å / Num. obs: 14593 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.9→3.12 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.8 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EMV Resolution: 2.9→74.54 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.871 / SU B: 52.69 / SU ML: 0.459 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.561 / 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: 56.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→74.54 Å
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Refine LS restraints |
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