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- PDB-9f64: Crystal structure of thiol peroxidase mutant (C94A) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9f64
TitleCrystal structure of thiol peroxidase mutant (C94A) in complex with Metro* (H. pylori
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
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
: / Thiol peroxidase
Similarity search - Component
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: to be published
Title: 5-Nitroimidazole ethers boost anti-Helicobacter pylori activity via a dual mode of action and effectively eradicate infections in vivo
Authors: 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.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9334
Polymers20,7071
Non-polymers2263
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint2 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.370, 71.480, 40.770
Angle α, β, γ (deg.)90.00, 115.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 20706.918 Da / Num. of mol.: 1 / Mutation: C94A
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: Chemical ChemComp-A1IAQ / 2-(5-azanyl-2-methyl-imidazol-1-yl)ethanol


Mass: 141.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, 0.01 M CoCl2, 20% PVP K15

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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: Jul 2, 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: 16754 / % possible obs: 95 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 14.3
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2627 / % possible all: 95

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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: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 13.316 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 837 5 %RANDOM
Rwork0.19694 ---
obs0.19764 15911 95.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.965 Å2
Baniso -1Baniso -2Baniso -3
1-5.39 Å20 Å23.95 Å2
2---6.2 Å2-0 Å2
3----2.06 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 5 39 1333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131311
X-RAY DIFFRACTIONr_bond_other_d0.0080.0161326
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.6481765
X-RAY DIFFRACTIONr_angle_other_deg1.2251.6023054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39924.82858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05315246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.541154
X-RAY DIFFRACTIONr_chiral_restr0.0470.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021472
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02277
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_it3.3465.19659
X-RAY DIFFRACTIONr_mcbond_other3.3425.184658
X-RAY DIFFRACTIONr_mcangle_it4.4417.792822
X-RAY DIFFRACTIONr_mcangle_other4.4397.797823
X-RAY DIFFRACTIONr_scbond_it3.3345.629651
X-RAY DIFFRACTIONr_scbond_other3.3325.631652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3218.241944
X-RAY DIFFRACTIONr_long_range_B_refined5.65862.1491405
X-RAY DIFFRACTIONr_long_range_B_other5.65962.0261399
X-RAY DIFFRACTIONr_rigid_bond_restr7.79232632
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
Rfree0.481 62 -
Rwork0.556 1172 -
obs--97.7 %
Refinement TLS params.Method: refined / Origin x: 14.6489 Å / Origin y: -0.9508 Å / Origin z: 4.5385 Å
111213212223313233
T0.0249 Å20.0041 Å2-0.0404 Å2-0.0673 Å20.0024 Å2--0.0739 Å2
L0.4122 °20.0302 °2-0.2681 °2-0.012 °2-0.0714 °2--0.5226 °2
S-0.0125 Å °-0.0051 Å °-0.0133 Å °-0.0028 Å °0.0019 Å °0.0087 Å °-0.0117 Å °0.0364 Å °0.0106 Å °

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