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- PDB-4tky: The complex structure of E. coli DsbA bound to a peptide at the D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tky | ||||||
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Title | The complex structure of E. coli DsbA bound to a peptide at the DsbA/DsbB interface | ||||||
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![]() | OXIDOREDUCTASE/PEPTIDE INHIBITOR / DsbA / DsbB / Dithiol oxidase / complex / DsbA/DsbB / peptide inhibitor / thioredoxin-related protein / OXIDOREDUCTASE-PEPTIDE INHIBITOR complex | ||||||
Function / homology | ![]() cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Premkumar, L. / Martin, J.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Peptide Inhibitors of the Escherichia coli DsbA Oxidative Machinery Essential for Bacterial Virulence. Authors: Duprez, W. / Premkumar, L. / Halili, M.A. / Lindahl, F. / Reid, R.C. / Fairlie, D.P. / Martin, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.9 KB | Display | ![]() |
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PDB format | ![]() | 132.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1fvkS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21324.141 Da / Num. of mol.: 4 / Fragment: UNP residues 20-208 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 739.794 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | ChemComp-ACE / #4: Chemical | ChemComp-NH2 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Ammonium sulfate, BIS-TRIS, Pentaerythritol ethoxylate PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40.8 Å / Num. obs: 28147 / % possible obs: 97.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 1.8 / % possible all: 92.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FVK Resolution: 2.5→34.402 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→34.402 Å
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Refine LS restraints |
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LS refinement shell |
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