+Open data
-Basic information
Entry | Database: PDB / ID: 2wlx | ||||||
---|---|---|---|---|---|---|---|
Title | Putative thiosulfate sulfurtransferase YnjE | ||||||
Components | PUTATIVE THIOSULFATE SULFURTRANSFERASE YNJE | ||||||
Keywords | TRANSFERASE / RHODANESE DOMAINS | ||||||
Function / homology | Function and homology information thiosulfate sulfurtransferase / sulfurtransferase activity / thiosulfate sulfurtransferase activity / periplasmic space Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å | ||||||
Authors | Declercq, J.P. / Smeets, A. / Depuydt, M. / Collet, J.F. | ||||||
Citation | Journal: To be Published Title: Structural Analysis of Ynje, a Putative Thiosulfate Sulfurtransferase Authors: Declercq, J.P. / Smeets, A. / Depuydt, M. / Collet, J.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wlx.cif.gz | 95.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wlx.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/2wlx ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wlx | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 47296.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P78067, thiosulfate sulfurtransferase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | WITHOUT SIGNAL SEQUENCE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
---|---|
Crystal grow | Temperature: 291 K / pH: 7.5 / Details: 20% PEG 10000, 0.1M HEPES PH 7.5, TEMP 18 C |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979609 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: May 17, 2009 / Details: SECOND CRYSTAL SAGITALLY BENT |
Radiation | Monochromator: FIRST CRYSTAL FLAT AND N2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979609 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 219109 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.9→2.1 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.5 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.9→39.77 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.452 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.27 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.77 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|