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Open data
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Basic information
Entry | Database: PDB / ID: 6pml | ||||||
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Title | Crystal Structure of EcDsbA in complex benzyl ether 23 | ||||||
![]() | Thiol:disulfide interchange protein DsbA | ||||||
![]() | OXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / OXIDOREDUCTASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Ilyichova, O.V. / Scanlon, M.J. | ||||||
![]() | ![]() Title: The Fragment-Based Development of a Benzofuran Hit as a New Class of Escherichia coli DsbA Inhibitors. Authors: Duncan, L.F. / Wang, G. / Ilyichova, O.V. / Scanlon, M.J. / Heras, B. / Abbott, B.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200 KB | Display | ![]() |
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PDB format | ![]() | 132 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pmfC ![]() 6pohC ![]() 6poiC ![]() 6poqC ![]() 6pvyC ![]() 6pvzC ![]() 1fvkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 21155.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Plasmid: B0013 / Production host: ![]() ![]() #2: Chemical | ChemComp-PEG / | #3: Chemical | ChemComp-OR4 / [ | #4: Chemical | ChemComp-CU / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.53 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 11-13 % PEG 8000, 5-7.5% glycerol, 100mM Na Cacodylate pH6.1, 1mM CuCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 1, 2014 |
Radiation | Monochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2→53.1 Å / Num. obs: 29762 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.68 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.056 / Rrim(I) all: 0.108 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4161 / CC1/2: 0.675 / Rpim(I) all: 0.394 / Rrim(I) all: 0.736 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FVK Resolution: 2→34.84 Å / SU ML: 0.252 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6782
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→34.84 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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