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Yorodumi- PDB-6ere: Crystal structure of a computationally designed colicin endonucle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ere | ||||||||||||
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Title | Crystal structure of a computationally designed colicin endonuclease and immunity pair colEdes3/Imdes3 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunity colicin | ||||||||||||
Function / homology | Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta / PHOSPHATE ION Function and homology information | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||||||||
Authors | Netzer, R. / Listov, D. / Dym, O. / Albeck, S. / Knop, O. / Fleishman, S.J. | ||||||||||||
Funding support | Israel, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: Ultrahigh specificity in a network of computationally designed protein-interaction pairs. Authors: Netzer, R. / Listov, D. / Lipsh, R. / Dym, O. / Albeck, S. / Knop, O. / Kleanthous, C. / Fleishman, S.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ere.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ere.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ere.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/6ere ftp://data.pdbj.org/pub/pdb/validation_reports/er/6ere | HTTPS FTP |
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-Related structure data
Related structure data | 6er6SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15199.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 11289.596 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-PO4 / | #4: 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 Å3/Da / Density % sol: 38.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 25% PEG 200, 50mM Sodium phosphate dibasic/ Citric acid pH=4.2 and 100mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→55.63 Å / Num. obs: 20578 / % possible obs: 98.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2005 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ER6 Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.193 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.247 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.2 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→50 Å
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Refine LS restraints |
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