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Open data
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Basic information
Entry | Database: PDB / ID: 2xpe | ||||||
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Title | Oxidised Thiol peroxidase (Tpx) from Yersinia pseudotuberculosis | ||||||
![]() | THIOL PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / 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. / 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 | ![]() | 72.2 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.4 KB | Display | ![]() |
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Full document | ![]() | 441.3 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xpdC ![]() 2yjhC ![]() 3zrdC ![]() 3zreC ![]() 1qxhS 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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Unit cell |
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Components
#1: Protein | Mass: 21397.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q66A71, UniProt: A0A0H3B2F9*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE INCLUDES THE NON-CLEAVED HIS6-TAG AND THE TEV PROTEASE RECOGNITIO | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.17 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.2 M TRI-POTASSIUM CITRATE, 20% PEG 3350, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 14, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38.27 Å / Num. obs: 11830 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.54 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 14.25 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QXH Resolution: 2.5→52.118 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.886 / SU B: 0 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 2.5 / ESU R: 0.901 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→52.118 Å
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Refine LS restraints |
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