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- PDB-3l9s: Crystal Structure of Salmonella enterica serovar Typhimurium DsbA -
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Open data
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Basic information
Entry | Database: PDB / ID: 3l9s | ||||||
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Title | Crystal Structure of Salmonella enterica serovar Typhimurium DsbA | ||||||
![]() | Thiol:disulfide interchange protein | ||||||
![]() | OXIDOREDUCTASE / thioredoxin-fold / DsbA / thiol-disulfide oxidoreductase / Disulfide bond / Redox-active center | ||||||
Function / homology | ![]() protein-disulfide reductase activity / cell redox homeostasis / periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Heras, B. / Jarrott, R. / Shouldice, S.R. / Guncar, G. | ||||||
![]() | ![]() Title: Structural and functional characterization of three DsbA paralogues from Salmonella enterica serovar typhimurium Authors: Heras, B. / Totsika, M. / Jarrott, R. / Shouldice, S.R. / Guncar, G. / Achard, M.E.S. / Wells, T.J. / Argente, M.P. / McEwan, A.G. / Schembri, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94 KB | Display | ![]() |
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PDB format | ![]() | 70.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.3 KB | Display | ![]() |
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Full document | ![]() | 416.4 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l9uC ![]() 3l9vC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 21215.115 Da / Num. of mol.: 1 / Fragment: UNP residues 19-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SL1344 / Gene: dsbA, STM3997 / Plasmid: pETLIC / Production host: ![]() ![]() References: UniProt: E1WE53, UniProt: P0A2H9*PLUS, protein disulfide-isomerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1M ammonium sulfate, 1% (w/v) polyethylene glycol 3350, 100mM 2,2-bis(hydroxymethyl)-2,2',2"-nitrilotriethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 15, 2008 / Details: mirrors |
Radiation | Monochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956667 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. all: 25131 / Num. obs: 25131 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.082 / Χ2: 1.064 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.188 / Num. unique all: 1176 / Χ2: 1.09 / % possible all: 87.4 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FVK Resolution: 1.58→21.058 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.888 / SU ML: 0.19 / σ(F): 1.91 / 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 / Bsol: 60.27 Å2 / ksol: 0.409 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.6 Å2 / Biso mean: 16.954 Å2 / Biso min: 6.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→21.058 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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