+Open data
-Basic information
Entry | Database: PDB / ID: 2vlo | ||||||
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Title | K97A mutant of E9 DNase domain in complex with Im9 | ||||||
Components |
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Keywords | PROTEIN BINDING / PROTEIN-BINDING / PROTEIN-PROTEIN INTERACTION / METAL-BINDING / ANTIMICROBIAL / BACTERIOCIN IMMUNITY / HYDROLASE / ANTIBIOTIC / BACTERIOCIN / ENDONUCLEASE / ZINC / COLICIN / PLASMID / NUCLEASE / HTH MOTIF | ||||||
Function / homology | Function and homology information 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 | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Keeble, A.H. / Joachimiak, L.A. / Mate, M.J. / Meenan, N. / Kirkpatrick, N. / Baker, D. / Kleanthous, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vlo.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vlo.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vlo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/2vlo ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vlo | HTTPS FTP |
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-Related structure data
Related structure data | 2vlnC 2vlpC 2vlqC 1emvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10525.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13479 | ||||||
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#2: Protein | Mass: 15061.918 Da / Num. of mol.: 1 / Fragment: DNASE DOMAIN, RESIDUES 450-582 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P09883 | ||||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | RESIDUE LYS 97 MUTATED TO ALA | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 44.51 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 19052 / % possible obs: 91.9 % / Observed criterion σ(I): 13.9 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.9 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMV Resolution: 1.8→27.95 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.859 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.143 / 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: 23.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.95 Å
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Refine LS restraints |
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