[English] 日本語
Yorodumi- PDB-4tky: The complex structure of E. coli DsbA bound to a peptide at the D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tky | ||||||
---|---|---|---|---|---|---|---|
Title | The complex structure of E. coli DsbA bound to a peptide at the DsbA/DsbB interface | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE/PEPTIDE INHIBITOR / DsbA / DsbB / Dithiol oxidase / complex / DsbA/DsbB / peptide inhibitor / thioredoxin-related protein / OXIDOREDUCTASE-PEPTIDE INHIBITOR complex | ||||||
Function / homology | Function and homology information cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Premkumar, L. / Martin, J.L. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4tky.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4tky.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 4tky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tky_validation.pdf.gz | 476.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4tky_full_validation.pdf.gz | 480.1 KB | Display | |
Data in XML | 4tky_validation.xml.gz | 30 KB | Display | |
Data in CIF | 4tky_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/4tky ftp://data.pdbj.org/pub/pdb/validation_reports/tk/4tky | HTTPS FTP |
-Related structure data
Related structure data | 1fvkS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-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.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEG4 #2: Protein/peptide | Mass: 739.794 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #3: Chemical | ChemComp-ACE / #4: Chemical | ChemComp-NH2 / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 52 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|