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Yorodumi- PDB-6er6: Crystal structure of a computationally designed colicin endonucle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6er6 | |||||||||
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Title | Crystal structure of a computationally designed colicin endonuclease and immunity pair colEdes7/Imdes7 | |||||||||
Components |
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Keywords | HYDROLASE / 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 Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Netzer, R. / Listov, D. / Dym, O. / Albeck, S. / Knop, O. / Fleishman, S.J. | |||||||||
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 | 6er6.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6er6.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 6er6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6er6_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 6er6_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 6er6_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 6er6_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/6er6 ftp://data.pdbj.org/pub/pdb/validation_reports/er/6er6 | HTTPS FTP |
-Related structure data
Related structure data | 6ereC 3u43S 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: 15371.396 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) |
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#2: Protein | Mass: 10950.970 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) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.66 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 12% PEG 1,500 and 0.05M MMT buffer pH=8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: AREA DETECTOR / Date: May 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→50.99 Å / Num. obs: 32715 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 6 / Num. unique obs: 3130 / % possible all: 97.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U43 Resolution: 1.6→25.51 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.281 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 82.37 Å2 / Biso mean: 28.368 Å2 / Biso min: 15.52 Å2
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Refinement step | Cycle: final / Resolution: 1.6→25.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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