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Open data
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Basic information
Entry | Database: PDB / ID: 6pc9 | |||||||||
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Title | Crystal Structure of EcDsbA in a complex with purified methylpiperazinone 6 | |||||||||
![]() | Thiol:disulfide interchange protein DsbA | |||||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / REFiLX / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE 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 | ![]() ![]() ![]() | |||||||||
![]() | Ilyichova, O.V. / Bentley, M. / Doak, B. / Scanlon, M.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiLX). Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, ...Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, B. / Doak, B.C. / Scanlon, M.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 66.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5qkcC ![]() 5qkdC ![]() 5qkeC ![]() 5qkfC ![]() 5qkgC ![]() 5qkhC ![]() 5qkiC ![]() 5qkjC ![]() 5qkkC ![]() 5qklC ![]() 5qkmC ![]() 5qknC ![]() 5qkoC ![]() 5qkpC ![]() 5qkqC ![]() 5qkrC ![]() 5qksC ![]() 5qktC ![]() 5qkuC ![]() 5qkvC ![]() 5qkwC ![]() 5qkxC ![]() 5qkyC ![]() 5qkzC ![]() 5ql0C ![]() 5ql1C ![]() 5ql2C ![]() 5ql3C ![]() 5ql4C ![]() 5ql5C ![]() 5ql6C ![]() 5ql7C ![]() 5ql8C ![]() 5ql9C ![]() 5qlaC ![]() 5qlbC ![]() 5qlcC ![]() 5qldC ![]() 5qleC ![]() 5qlfC ![]() 5qlgC ![]() 5qlhC ![]() 5qliC ![]() 5qljC ![]() 5qlkC ![]() 5qllC ![]() 5qlmC ![]() 5qlnC ![]() 5qloC ![]() 5qlpC ![]() 5qlqC ![]() 5qlrC ![]() 5qlsC ![]() 5qltC ![]() 5qluC ![]() 5qlvC ![]() 5qlwC ![]() 5qlxC ![]() 5qlyC ![]() 5qlzC ![]() 5qm0C ![]() 5qm1C ![]() 5qm2C ![]() 5qm3C ![]() 5qm4C ![]() 5qm5C ![]() 5qm6C ![]() 5qm7C ![]() 5qm8C ![]() 5qm9C ![]() 5qmaC ![]() 5qmbC ![]() 5qmcC ![]() 5qmdC ![]() 5qmeC ![]() 5qmfC ![]() 5qmgC ![]() 5qmhC ![]() 5qmiC ![]() 5qmjC ![]() 5qmkC ![]() 5qmlC ![]() 5qmmC ![]() 5qmnC ![]() 5qmoC ![]() 5qmpC ![]() 5qmqC ![]() 5qmrC ![]() 5qmsC ![]() 5qmtC ![]() 5qmuC ![]() 5qmvC ![]() 5qmwC ![]() 5qmxC ![]() 5qmyC ![]() 5qmzC ![]() 5qn0C ![]() 5qn1C ![]() 5qn2C ![]() 5qn3C ![]() 5qn4C ![]() 5qn5C ![]() 5qn6C ![]() 5qn7C ![]() 5qn8C ![]() 5qn9C ![]() 5qnaC ![]() 5qnbC ![]() 5qncC ![]() 5qndC ![]() 5qneC ![]() 5qnfC ![]() 5qngC ![]() 5qnhC ![]() 5qniC ![]() 5qnjC ![]() 5qnkC ![]() 5qnlC ![]() 5qnmC ![]() 5qnnC ![]() 5qnoC ![]() 5qnpC ![]() 5qnqC ![]() 5qnrC ![]() 5qnsC ![]() 5qntC ![]() 5qnuC ![]() 5qnvC ![]() 5qnwC ![]() 5qnxC ![]() 5qnyC ![]() 5qnzC ![]() 5qo0C ![]() 5qo1C ![]() 5qo2C ![]() 5qo3C ![]() 5qo4C ![]() 5qo5C ![]() 5qo6C ![]() 5qo7C ![]() 5qo8C ![]() 5qo9C ![]() 5qoaC ![]() 5qobC ![]() 5qocC ![]() 5qodC ![]() 5qoeC ![]() 5qofC ![]() 5qogC ![]() 6pbiC ![]() 6pd7C ![]() 6pdhC ![]() 6pg1C ![]() 6pg2C ![]() 6pgjC ![]() 6piqC ![]() 6pliC ![]() 6whdC ![]() 1dsbS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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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-O7P / | #3: Chemical | ChemComp-PGE / | #4: 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: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 25-35 % PEG MME 2000, 100-300 mM KBr |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2018 |
Radiation | Monochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.52 Å / Num. obs: 18356 / % possible obs: 99.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Χ2: 1.04 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.735 / Num. unique obs: 1730 / CC1/2: 0.891 / Rpim(I) all: 0.306 / Rrim(I) all: 0.797 / Χ2: 0.99 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DSB Resolution: 2.3→43.1 Å / SU ML: 0.2637 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7487 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 49.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→43.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.925537327094 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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