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Yorodumi- PDB-5ew5: Crystal Structure of Colicin E9 In Complex with Its Immunity Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ew5 | ||||||
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Title | Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 | ||||||
Components |
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Keywords | HYDROLASE / colicin / complex / toxin | ||||||
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: 3.2 Å | ||||||
Authors | Klein, A. / Wojdyla, J.A. / Kleanthous, C. | ||||||
Citation | Journal: Biochem.J. / Year: 2016 Title: Structural and biophysical analysis of nuclease protein antibiotics. Authors: Klein, A. / Wojdyla, J.A. / Joshi, A. / Josts, I. / McCaughey, L.C. / Housden, N.G. / Kaminska, R. / Byron, O. / Walker, 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 | 5ew5.cif.gz | 435.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ew5.ent.gz | 356.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ew5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/5ew5 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/5ew5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 61563.145 Da / Num. of mol.: 4 / Mutation: Y324C, L447C, D448A, K449M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: col, cei / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P09883, Hydrolases; Acting on ester bonds #2: Protein | Mass: 10663.653 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: imm, ceiE9 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13479 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 1.3M sodium malonate, PEG3350 / PH range: 4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→29.6 Å / Num. obs: 53941 / % possible obs: 99.1 % / Redundancy: 3.5 % / Rsym value: 0.0127 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 3.37 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.694 / % possible all: 95.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JCH and 2GZG Resolution: 3.2→29.6 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.894 / SU B: 31.06 / SU ML: 0.491 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.384 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→29.6 Å
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Refine LS restraints |
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