[English] 日本語
Yorodumi- PDB-6eez: Crystal Structure of the thiol-disulfide exchange protein alpha-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eez | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the thiol-disulfide exchange protein alpha-DsbA2 from Wolbachia pipientis | ||||||
Components | DsbA-like disulfide oxidoreductase | ||||||
Keywords | ISOMERASE / Thiol-disulfide exchange protein | ||||||
Function / homology | Thioredoxin / Thioredoxin-like fold / Thioredoxin-like superfamily / DsbA-like disulfide oxidoreductase Function and homology information | ||||||
Biological species | Wolbachia endosymbiont of Drosophila melanogaster (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Walden, P.M. / Lakshmanane, P. / King, G.J. / Martin, J.L. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: The atypical thiol-disulfide exchange protein alpha-DsbA2 from Wolbachia pipientis is a homotrimeric disulfide isomerase. Authors: Walden, P.M. / Whitten, A.E. / Premkumar, L. / Halili, M.A. / Heras, B. / King, G.J. / Martin, J.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6eez.cif.gz | 420.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6eez.ent.gz | 365.8 KB | Display | PDB format |
PDBx/mmJSON format | 6eez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/6eez ftp://data.pdbj.org/pub/pdb/validation_reports/ee/6eez | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21122.807 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wolbachia endosymbiont of Drosophila melanogaster (bacteria) Gene: WD_1312 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q73FL6 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.8 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Tris pH 7.5, 200 mM NaCl and 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.543 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.543 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→19.77 Å / Num. obs: 35424 / % possible obs: 99.04 % / Redundancy: 3.8 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.038 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 3209 / Rsym value: 0.187 / % possible all: 97.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→19.768 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.65
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→19.768 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|