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- PDB-9f5v: Crystal structure of thiol peroxidase from Helicobacter pylori (H... -

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Basic information

Entry
Database: PDB / ID: 9f5v
TitleCrystal structure of thiol peroxidase from Helicobacter pylori (HpTx, reduced)
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / Stress Response / Detoxification / Active Site Analysis / Protein Inhibitor Interactions / Catalysis / Drug Target
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFiedler, M.K. / Gong, R. / Fuchs, S. / Rox, K. / Friedrich, V. / Pfeiffer, D. / Reinhardt, T. / Mibus, C. / Huber, M. / Hess, C. ...Fiedler, M.K. / Gong, R. / Fuchs, S. / Rox, K. / Friedrich, V. / Pfeiffer, D. / Reinhardt, T. / Mibus, C. / Huber, M. / Hess, C. / Mejias-Luque, R. / Gerhard, M. / Groll, M. / Sieber, S.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309 - 325871075 Germany
CitationJournal: Nat Microbiol / Year: 2026
Title: Metronidazole and ether derivatives target Helicobacter pylori via simultaneous stress induction and inhibition.
Authors: Fiedler, M.K. / Pandler, M.S.I. / Gong, R. / Fuchs, S. / Rox, K. / Friedrich, V. / Pfeiffer, D. / Singh, D. / Reinhardt, T. / Mibus, C. / Huber, M. / Hess, C.R. / Mejias-Luque, R. / Gerhard, ...Authors: Fiedler, M.K. / Pandler, M.S.I. / Gong, R. / Fuchs, S. / Rox, K. / Friedrich, V. / Pfeiffer, D. / Singh, D. / Reinhardt, T. / Mibus, C. / Huber, M. / Hess, C.R. / Mejias-Luque, R. / Gerhard, M. / Groll, M. / Sieber, S.A.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)41,4782
Polymers41,4782
Non-polymers00
Water1,42379
1
A: Thiol peroxidase


Theoretical massNumber of molelcules
Total (without water)20,7391
Polymers20,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol peroxidase


Theoretical massNumber of molelcules
Total (without water)20,7391
Polymers20,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.530, 68.630, 64.380
Angle α, β, γ (deg.)90.00, 98.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20738.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: tpx, HP_0390 / Production host: Escherichia coli (E. coli)
References: UniProt: O25151, thioredoxin-dependent peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, 30% PEG 400 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 34071 / % possible obs: 96.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.1
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5224 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.502 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1703 5 %RANDOM
Rwork0.18256 ---
obs0.18436 32361 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.021 Å2
Baniso -1Baniso -2Baniso -3
1--4 Å20 Å2-0.14 Å2
2--2.93 Å20 Å2
3---1.06 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 0 79 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132586
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162607
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.6293483
X-RAY DIFFRACTIONr_angle_other_deg1.1441.5856013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1835327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7224.828116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07915492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.592158
X-RAY DIFFRACTIONr_chiral_restr0.0490.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
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_it1.963.4081314
X-RAY DIFFRACTIONr_mcbond_other1.9563.4071313
X-RAY DIFFRACTIONr_mcangle_it2.6815.1111639
X-RAY DIFFRACTIONr_mcangle_other2.6815.1121640
X-RAY DIFFRACTIONr_scbond_it2.0583.8351272
X-RAY DIFFRACTIONr_scbond_other2.0573.8351273
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7465.5751845
X-RAY DIFFRACTIONr_long_range_B_refined3.54639.6422686
X-RAY DIFFRACTIONr_long_range_B_other3.53739.5912679
X-RAY DIFFRACTIONr_rigid_bond_restr0.61835193
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 125 -
Rwork0.292 2368 -
obs--96.33 %
Refinement TLS params.

S11: -0.0026 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)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)
10.1476-0.0002-0.03630.04960.01570.1209-0.0151-0.00110.0025-0.00280.001-0.00280.00170.00540.0285-0.0002-0.0010.0020.00080.002414.154-0.56492.018
20.0752-0.0060.02160.05760.02550.08790.0073-0.00590.0005-0.00010.0016-0.00360.00010.00270.0286-0.0003-0.00020.0008-0.00060.001410.9839-3.0618-28.2653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 166
2X-RAY DIFFRACTION2B2 - 165

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