[English] 日本語
Yorodumi
- PDB-5ijt: Human Peroxiredoxin 2 Oxidized (SS) -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of T cell differentiation / leukocyte activation / regulation of hydrogen peroxide metabolic process / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin-dependent peroxiredoxin / 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 / negative regulation of T cell differentiation / leukocyte activation / regulation of hydrogen peroxide metabolic process / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin-dependent peroxiredoxin / 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 / cell redox homeostasis / thymus development / 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 / 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 / Glutaredoxin / Glutaredoxin ...: / 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
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more