+Open data
-Basic information
Entry | Database: PDB / ID: 3i43 | ||||||
---|---|---|---|---|---|---|---|
Title | Escherichia coli Thiol peroxidase (Tpx) wild type disulfide form | ||||||
Components | Thiol peroxidase | ||||||
Keywords | OXIDOREDUCTASE / TPX / PEROXIREDOXIN / PEROXIDASE / ANTIOXIDANT | ||||||
Function / homology | Function and homology information hydroperoxide reductase activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to oxidative stress / periplasmic space / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Difference fourier based on isomorphous starting model / Resolution: 2.8 Å | ||||||
Authors | Hall, A. / Karplus, P.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural changes common to catalysis in the Tpx peroxiredoxin subfamily. Authors: Hall, A. / Sankaran, B. / Poole, L.B. / Karplus, P.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3i43.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3i43.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 3i43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i43_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3i43_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 3i43_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 3i43_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/3i43 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/3i43 | HTTPS FTP |
-Related structure data
Related structure data | 3hvsSC 3hvvC 3hvxC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17717.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: See Baker and Poole, 2003. / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 (XL-1 Blue) / Gene: b1324, JW1317, tpx, yzzJ / Plasmid: pPROK1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue / References: UniProt: P0A862, peroxiredoxin #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.15 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 20% (w/v) PEG-8000, 0.1 M phosphate citrate, 0.2 M sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 28, 2008 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→37.36 Å / Num. obs: 7832 / % possible obs: 96.88 % / Redundancy: 2.9 % / Rsym value: 0.105 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1267 / Rsym value: 0.368 / % possible all: 98 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: Difference fourier based on isomorphous starting model Starting model: PDB ENTRY 3HVS Resolution: 2.8→37.36 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.91 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: This is not a stand alone structure, but is derived from the higher resolution structure 3HVS by a simple rigid body refinement combined with manual adjustment and geometry optimization of ...Details: This is not a stand alone structure, but is derived from the higher resolution structure 3HVS by a simple rigid body refinement combined with manual adjustment and geometry optimization of only the catalytic residues Cys61 and Cys95. This data set is at much lower resolution and was only used to confirm the presence of an intact disulfide. The conformation of Cys61 and Cys95 from this structure has been added as an alternate conformation with zero occupancy to the higher resolution structure 3HVS and we recommend use of that structure rather than this one.
| ||||||||||||||||||||
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: 22.84 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→37.36 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
|