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- PDB-2yjh: Thiol Peroxidase from Yersinia Psuedotuberculosis, inactive mutan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yjh | ||||||
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Title | Thiol Peroxidase from Yersinia Psuedotuberculosis, inactive mutant C61S | ||||||
![]() | THIOL PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / ATYPICAL 2-CYS PEROXIREDOXIN / PEROXIDE PROTECTION / ANTI- VIRULENCE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beckham, K.S.H. / Gabrielsen, M. / Wang, D. / Roe, A.J. | ||||||
![]() | ![]() Title: Structural Characterisation of Tpx from Yersinia Pseudotuberculosis Reveals Insights Into the Binding of Salicylidene Acylhydrazide Compounds. Authors: Gabrielsen, M. / Beckham, K.S.H. / Feher, V.A. / Zetterstrom, C.E. / Wang, D. / Muller, S. / Elofsson, M. / Amaro, R.E. / Byron, O. / Roe, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.2 KB | Display | ![]() |
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PDB format | ![]() | 28.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.9 KB | Display | ![]() |
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Full document | ![]() | 436.2 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 9.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xpdSC ![]() 2xpeC ![]() 3zrdC ![]() 3zreC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21381.211 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q66A71, peroxiredoxin, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.95 % / Description: NONE |
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Crystal grow | pH: 7.6 / Details: 12% PEG 3350, 0.05 M NA, HEPES PH 7.0, 1% TRYPTONE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 25, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→56.32 Å / Num. obs: 6151 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 72.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XPD Resolution: 2.55→56.32 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.871 / SU B: 19.246 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R: 0.897 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 62.083 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→56.32 Å
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Refine LS restraints |
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