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- PDB-7weu: Crystal structure of Peroxiredoxin I in complex with compound 19-048 -

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Basic information

Entry
Database: PDB / ID: 7weu
TitleCrystal structure of Peroxiredoxin I in complex with compound 19-048
ComponentsPeroxiredoxin-1
KeywordsOXIDOREDUCTASE / Inhibitor / Complex / Peroxiredoxin
Function / homology
Function and homology information


leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell mediated cytotoxicity / natural killer cell activation / erythrocyte homeostasis / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of stress-activated MAPK cascade / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models ...leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell mediated cytotoxicity / natural killer cell activation / erythrocyte homeostasis / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of stress-activated MAPK cascade / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / canonical NF-kappaB signal transduction / removal of superoxide radicals / cell redox homeostasis / skeletal system development / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / melanosome / fibroblast proliferation / response to oxidative stress / cell population proliferation / cadherin binding / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Unknown ligand / Peroxiredoxin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsZhang, H. / Luo, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903538 China
CitationJournal: Signal Transduct Target Ther / Year: 2023
Title: Celastrol suppresses colorectal cancer via covalent targeting peroxiredoxin 1.
Authors: Xu, H. / Zhao, H. / Ding, C. / Jiang, D. / Zhao, Z. / Li, Y. / Ding, X. / Gao, J. / Zhou, H. / Luo, C. / Chen, G. / Zhang, A. / Xu, Y. / Zhang, H.
History
DepositionDec 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxiredoxin-1
B: Peroxiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7773
Polymers38,6742
Non-polymers1031
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-9 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.925, 77.820, 81.152
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 Peroxiredoxin-1 / / Natural killer cell-enhancing factor A / NKEF-A / Proliferation-associated gene protein / PAG / ...Natural killer cell-enhancing factor A / NKEF-A / Proliferation-associated gene protein / PAG / Thioredoxin peroxidase 2 / Thioredoxin-dependent peroxide reductase 2 / Thioredoxin-dependent peroxiredoxin 1


Mass: 19337.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX1, PAGA, PAGB, TDPX2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q06830, thioredoxin-dependent peroxiredoxin
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Tacsimate pH 8.0 (v/v) and 20% PEG3350 (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.81→35.98 Å / Num. obs: 37334 / % possible obs: 99.94 % / Redundancy: 13.3 % / Biso Wilson estimate: 17.88 Å2 / CC1/2: 0.999 / Net I/σ(I): 33.54
Reflection shellResolution: 1.814→1.879 Å / Num. unique obs: 3669 / CC1/2: 0.991

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XCS

4xcs


Resolution: 1.81→35.98 Å / SU ML: 0.133 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1955 1854 4.97 %
Rwork0.1556 35457 -
obs0.1575 37311 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.83 Å2
Refinement stepCycle: LAST / Resolution: 1.81→35.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 40 446 3102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612726
X-RAY DIFFRACTIONf_angle_d0.90693703
X-RAY DIFFRACTIONf_chiral_restr0.0631404
X-RAY DIFFRACTIONf_plane_restr0.0068476
X-RAY DIFFRACTIONf_dihedral_angle_d3.16221607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.20921490.16482651X-RAY DIFFRACTION100
1.86-1.920.20641440.162701X-RAY DIFFRACTION100
1.92-1.980.19191430.15582694X-RAY DIFFRACTION100
1.98-2.050.19751530.1522693X-RAY DIFFRACTION100
2.05-2.130.20351350.15392684X-RAY DIFFRACTION99.96
2.13-2.230.20911320.15472709X-RAY DIFFRACTION100
2.23-2.350.19061240.16112729X-RAY DIFFRACTION100
2.35-2.490.19881530.1692691X-RAY DIFFRACTION99.96
2.49-2.690.18871670.16512710X-RAY DIFFRACTION100
2.69-2.960.19321370.16922747X-RAY DIFFRACTION100
2.96-3.380.22741360.16062755X-RAY DIFFRACTION100
3.38-4.260.18831120.13892818X-RAY DIFFRACTION100
4.26-35.980.17551690.14852875X-RAY DIFFRACTION99.61

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