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- PDB-5ijt: Human Peroxiredoxin 2 Oxidized (SS) -

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Basic information

Entry
Database: PDB / ID: 5ijt
TitleHuman Peroxiredoxin 2 Oxidized (SS)
ComponentsPeroxiredoxin-2
KeywordsOXIDOREDUCTASE / decamer disulfide bond
Function / homology
Function and homology information


respiratory burst involved in inflammatory response / leukocyte activation / negative regulation of T cell differentiation / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species ...respiratory burst involved in inflammatory response / leukocyte activation / negative regulation of T cell differentiation / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / T cell homeostasis / antioxidant activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of blood coagulation / T cell proliferation / extrinsic apoptotic signaling pathway / removal of superoxide radicals / thymus development / cell redox homeostasis / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / cellular response to oxidative stress / regulation of apoptotic process / response to oxidative stress / response to lipopolysaccharide / positive regulation of MAPK cascade / negative regulation of apoptotic process / extracellular exosome / cytoplasm / cytosol
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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å
AuthorsHaynes, A.C. / Bolduc, J.A. / Lowther, W.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM072866 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Novel hyperoxidation resistance motifs in 2-Cys peroxiredoxins.
Authors: Bolduc, J.A. / Nelson, K.J. / Haynes, A.C. / Lee, J. / Reisz, J.A. / Graff, A.H. / Clodfelter, J.E. / Parsonage, D. / Poole, L.B. / Furdui, C.M. / Lowther, W.T.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 27, 2019Group: Data collection / Database references / Polymer sequence
Category: citation / citation_author / entity_poly
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _entity_poly.pdbx_target_identifier
Revision 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin-2
B: Peroxiredoxin-2
C: Peroxiredoxin-2
D: Peroxiredoxin-2
E: Peroxiredoxin-2
F: Peroxiredoxin-2
G: Peroxiredoxin-2
H: Peroxiredoxin-2
I: Peroxiredoxin-2
J: Peroxiredoxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,45114
Polymers219,18910
Non-polymers2624
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20520 Å2
ΔGint-190 kcal/mol
Surface area70130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.014, 198.784, 116.523
Angle α, β, γ (deg.)90.000, 96.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peroxiredoxin-2 / Natural killer cell-enhancing factor B / NKEF-B / PRP / Thiol-specific antioxidant protein / TSA / ...Natural killer cell-enhancing factor B / NKEF-B / PRP / Thiol-specific antioxidant protein / TSA / Thioredoxin peroxidase 1 / Thioredoxin-dependent peroxide reductase 1


Mass: 21918.887 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX2, NKEFB, TDPX1 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / References: UniProt: P32119, peroxiredoxin
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 6.1% PEG 3350, 0.1 M sodium acetate pH 4.1, 0.2 M zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.148→44.5 Å / Num. obs: 122120 / % possible obs: 99.6 % / Observed criterion σ(I): 2.8 / Redundancy: 6.6 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.1
Reflection shellResolution: 2.148→2.23 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.8 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QMV

1qmv


Resolution: 2.148→44.463 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 3611 2.96 %
Rwork0.2066 118509 -
obs0.2081 122120 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 292.86 Å2 / Biso mean: 78.1382 Å2 / Biso min: 33.42 Å2
Refinement stepCycle: final / Resolution: 2.148→44.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13141 0 4 95 13240
Biso mean--108.4 51.31 -
Num. residues----1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01613436
X-RAY DIFFRACTIONf_angle_d1.33218214
X-RAY DIFFRACTIONf_chiral_restr0.0712032
X-RAY DIFFRACTIONf_plane_restr0.012361
X-RAY DIFFRACTIONf_dihedral_angle_d12.1797962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1482-2.17640.37391280.31514235436391
2.1764-2.20620.35761370.29244844621100
2.2062-2.23780.31921380.27545634701100
2.2378-2.27120.34621420.271246484790100
2.2712-2.30660.32461370.259744724609100
2.3066-2.34450.29831380.263845474685100
2.3445-2.38490.31021400.268946174757100
2.3849-2.42820.33441390.254245214660100
2.4282-2.47490.30861390.263745734712100
2.4749-2.52550.29941380.255845494687100
2.5255-2.58040.35051390.247245464685100
2.5804-2.64040.31231420.248746414783100
2.6404-2.70640.31431380.246145274665100
2.7064-2.77960.32571410.255546054746100
2.7796-2.86140.29131370.23945074644100
2.8614-2.95370.25321410.231646154756100
2.9537-3.05920.30421380.231145534691100
3.0592-3.18170.27341390.229745564695100
3.1817-3.32640.29581410.23746504791100
3.3264-3.50180.25281370.222145044641100
3.5018-3.72110.2431410.211145894730100
3.7211-4.00820.28341380.201745774715100
4.0082-4.41120.21711410.166546044745100
4.4112-5.04880.19111400.150946134753100
5.0488-6.3580.2261400.189345824722100
6.358-44.47210.22321420.176446314773100

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