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- PDB-3zrd: Oxidised Thiol peroxidase (Tpx) from Yersinia pseudotuberculosis -

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Basic information

Entry
Database: PDB / ID: 3zrd
TitleOxidised 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
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...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: 1.74 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
B: THIOL PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)42,7952
Polymers42,7952
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-8.2 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.180, 62.560, 88.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THIOL PEROXIDASE


Mass: 21397.277 Da / Num. of mol.: 2
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 / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONTAINS 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: 2.24 Å3/Da / Density % sol: 45.2 % / Description: NONE
Crystal growDetails: 0.2 M TRIPOTASSIUM CITRATE, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793
DetectorType: ADSC CCD / 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: 1.82→28.09 Å / Num. obs: 28072 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 26.05 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.1
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.2 / % possible all: 92.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XPE

2xpe


Resolution: 1.74→28.09 Å / Cor.coef. Fo:Fc: 0.9508 / Cor.coef. Fo:Fc free: 0.9357 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1572 5.04 %RANDOM
Rwork0.1951 ---
obs0.1969 22213 96.04 %-
Displacement parametersBiso mean: 32.95 Å2
Baniso -1Baniso -2Baniso -3
1-3.8535 Å20 Å20 Å2
2---1.8198 Å20 Å2
3----2.0337 Å2
Refinement stepCycle: LAST / Resolution: 1.74→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 0 199 2681
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092555HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.083475HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d865SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes373HARMONIC5
X-RAY DIFFRACTIONt_it2555HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion16.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion352SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3199SEMIHARMONIC4
LS refinement shellResolution: 1.74→1.8 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2818 126 5.74 %
Rwork0.227 2069 -
all0.2303 2195 -
obs--96.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2454-0.7331-0.52821.7440.53590.953-0.0801-0.1895-0.15570.05320.05370.02420.03450.02920.0263-0.06290.0170.0108-0.0430.0157-0.0792-5.63916.256916.5948
24.96761.1713-0.5551.624-0.04020.8916-0.20780.0241-0.2476-0.20260.1518-0.22390.0568-0.00760.0561-0.0770.01020.0559-0.1073-0.0099-0.055924.0072-1.00868.1513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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