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Yorodumi- PDB-1v13: CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v13 | ||||||
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Title | CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS) | ||||||
Components | COLICIN E9 | ||||||
Keywords | HYDROLASE / HOMING ENDONUCLEASES / COLICINS / BETA-BETA-ALPHA METAL ANTIBIOTIC / BACTERIOCIN / ENDONUCLEASE MOTIF / H-N-H MOTIF | ||||||
Function / homology | Function and homology information 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 | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mate, M.J. / Kleanthous, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases Authors: Mate, M.J. / Kleanthous, C. #1: Journal: J.Mol.Biol. / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v13.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v13.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 1v13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/1v13 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/1v13 | HTTPS FTP |
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-Related structure data
Related structure data | 1v14C 1v15C 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: 15052.951 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PTRC 99A (PRJ352) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P09883, Hydrolases; Acting on ester bonds #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.8 % |
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Crystal grow | pH: 5.8 / Details: pH 5.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9645 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9645 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 18519 / % possible obs: 91.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.8 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMV Resolution: 2→50.64 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.299 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.209 / 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: 52.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50.64 Å
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Refine LS restraints |
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