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- PDB-8zwt: Crystal structure of atypical two cysteine thiol peroxidase from ... -

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Basic information

Entry
Database: PDB / ID: 8zwt
TitleCrystal structure of atypical two cysteine thiol peroxidase from Staphylococcus aureus
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / Two-Cysteine Thiol peroxidase / Staphylococcus aureus / Substrate free form
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Thiol peroxidase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsShukla, M. / Maji, S. / Yadav, V.K. / Bhattacharyya, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)SRG/2020/001353 India
CitationJournal: To Be Published
Title: Crystal structure of atypical two cysteine thiol peroxidase from Staphylococcus aureus
Authors: Shukla, M. / Maji, S. / Yadav, V.K. / Bhattacharyya, S.
History
DepositionJun 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol peroxidase
B: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2013
Polymers36,0462
Non-polymers1541
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-12 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.061, 71.911, 88.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Thiol peroxidase / Tpx / Peroxiredoxin tpx / Prx / Thioredoxin peroxidase / Thioredoxin-dependent peroxiredoxin


Mass: 18023.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: tpx, SACOL1762 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5HF61, thioredoxin-dependent peroxiredoxin
#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate tribasic dihydrate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.85→44.16 Å / Num. obs: 27499 / % possible obs: 98.4 % / Redundancy: 7 % / Biso Wilson estimate: 25.95 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.9
Reflection shellResolution: 1.85→1.95 Å / Num. unique obs: 3560 / CC1/2: 0.819 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSQ

1psq


Resolution: 1.85→37.25 Å / SU ML: 0.1894 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 1329 4.86 %
Rwork0.1697 26019 -
obs0.1716 27348 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.73 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 8 266 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122596
X-RAY DIFFRACTIONf_angle_d1.21363522
X-RAY DIFFRACTIONf_chiral_restr0.0677406
X-RAY DIFFRACTIONf_plane_restr0.0099463
X-RAY DIFFRACTIONf_dihedral_angle_d7.3717354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.2997890.23322530X-RAY DIFFRACTION85.98
1.92-2.010.26421670.20522854X-RAY DIFFRACTION99.57
2.01-2.120.23031350.19372925X-RAY DIFFRACTION99.84
2.12-2.250.25451660.1882890X-RAY DIFFRACTION99.58
2.25-2.420.25581600.17982892X-RAY DIFFRACTION99.64
2.42-2.670.2271660.17772915X-RAY DIFFRACTION99.52
2.67-3.050.20851390.18372932X-RAY DIFFRACTION99.48
3.05-3.850.17461560.15022969X-RAY DIFFRACTION98.89
3.85-37.250.17671510.15263112X-RAY DIFFRACTION99.51
Refinement TLS params.Method: refined / Origin x: 0.791132926036 Å / Origin y: -5.07415783847 Å / Origin z: 12.9555276368 Å
111213212223313233
T0.198107829873 Å20.00987408337858 Å2-0.0341166149171 Å2-0.136015673631 Å2-0.0130069611451 Å2--0.187829269837 Å2
L1.74491608201 °20.116743313557 °2-0.936767519597 °2-0.603203791385 °2-0.393526230017 °2--1.52040621571 °2
S-0.00253788515919 Å °0.0562048286173 Å °-0.0125474895859 Å °0.0237938972517 Å °-0.00966281640348 Å °-0.0263867637432 Å °-0.0099806073234 Å °0.00745958236514 Å °0.0111358897318 Å °
Refinement TLS groupSelection details: all

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