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Open data
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Basic information
Entry | Database: PDB / ID: 3zre | ||||||
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Title | Reduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis | ||||||
![]() | THIOL PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / 2CYS PEROXIREDOXIN / THIOREDOXIN-FOLD / ROS PROTECTION | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gabrielsen, M. / Zetterstrom, C.E. / Wang, D. / Elofsson, M. / 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. #1: Journal: J.Biol.Chem. / Year: 2011 Title: Identification of Bacterial Target Proteins for the Salicylidene Acylhydrazide Class of Virulence- Blocking Compounds. Authors: Wang, D. / Zetterstrom, C.E. / Gabrielsen, M. / Beckham, K.S.H. / Tree, J.J. / Macdonald, S.E. / Byron, O. / Mitchell, T.J. / Gally, D.L. / Herzyk, P. / Mahajan, A. / Uvell, H. / Burchmore, ...Authors: Wang, D. / Zetterstrom, C.E. / Gabrielsen, M. / Beckham, K.S.H. / Tree, J.J. / Macdonald, S.E. / Byron, O. / Mitchell, T.J. / Gally, D.L. / Herzyk, P. / Mahajan, A. / Uvell, H. / Burchmore, R. / Smith, B.O. / Elofsson, M. / 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 | ![]() | 45.1 KB | Display | ![]() |
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PDB format | ![]() | 30.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.4 KB | Display | ![]() |
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Full document | ![]() | 430.3 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xpdSC ![]() 2xpeC ![]() 2yjhC ![]() 3zrdC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 21397.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q66A71, UniProt: A0A0H3B2F9*PLUS, peroxiredoxin |
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#2: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ENCODES HISTIDINE TAG AND TEV PROTEASE CLEAVAGE SITE. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.29 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM MALONATE PH 5, 12% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2010 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→47.15 Å / Num. obs: 8685 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XPD Resolution: 2.35→56.3 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.415 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.249 / 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: 59.604 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→56.3 Å
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Refine LS restraints |
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