[English] 日本語
Yorodumi- PDB-3l9s: Crystal Structure of Salmonella enterica serovar Typhimurium DsbA -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l9s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Salmonella enterica serovar Typhimurium DsbA | ||||||
Components | Thiol:disulfide interchange protein | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin-fold / DsbA / thiol-disulfide oxidoreductase / Disulfide bond / Redox-active center | ||||||
Function / homology | Function and homology information protein-disulfide reductase activity / cell redox homeostasis / periplasmic space Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å | ||||||
Authors | Heras, B. / Jarrott, R. / Shouldice, S.R. / Guncar, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3l9s.cif.gz | 94 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3l9s.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3l9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l9s_validation.pdf.gz | 415.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3l9s_full_validation.pdf.gz | 416.4 KB | Display | |
Data in XML | 3l9s_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 3l9s_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/3l9s ftp://data.pdbj.org/pub/pdb/validation_reports/l9/3l9s | HTTPS FTP |
-Related structure data
Related structure data | 3l9uC 3l9vC 1fvkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: SL1344 / Gene: dsbA, STM3997 / Plasmid: pETLIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)/plyss References: UniProt: E1WE53, UniProt: P0A2H9*PLUS, protein disulfide-isomerase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956667 Å |
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: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→21.058 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
|