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- PDB-3zre: Reduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis -

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Basic information

Entry
Database: PDB / ID: 3zre
TitleReduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis
ComponentsTHIOL PEROXIDASE
KeywordsOXIDOREDUCTASE / 2CYS PEROXIREDOXIN / THIOREDOXIN-FOLD / ROS PROTECTION
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to oxidative stress
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol peroxidase / Thiol peroxidase
Similarity search - Component
Biological speciesYERSINIA PSEUDOTUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGabrielsen, M. / Zetterstrom, C.E. / Wang, D. / Elofsson, M. / Roe, A.J.
Citation
Journal: Plos One / Year: 2012
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
DepositionJun 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOL PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)21,3971
Polymers21,3971
Non-polymers00
Water21612
1
A: THIOL PEROXIDASE

A: THIOL PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)42,7952
Polymers42,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area1460 Å2
ΔGint-9.9 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.008, 65.008, 86.284
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

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Components

#1: Protein THIOL PEROXIDASE


Mass: 21397.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: YPIII / Plasmid: PET-151 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q66A71, UniProt: A0A0H3B2F9*PLUS, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ENCODES HISTIDINE TAG AND TEV PROTEASE CLEAVAGE SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.29 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM MALONATE PH 5, 12% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XPD

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.27337 412 4.8 %RANDOM
Rwork0.23343 ---
obs0.23535 8251 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.604 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20.94 Å20 Å2
2--1.88 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.35→56.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 0 12 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.971646
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1595164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.67325.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16315185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.186155
X-RAY DIFFRACTIONr_chiral_restr0.120.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021896
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9641.5817
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71221307
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2353390
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3524.5339
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 33 -
Rwork0.289 607 -
obs--100 %

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