[English] 日本語
Yorodumi
- PDB-4xcs: Human peroxiredoxin-1 C83S mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xcs
TitleHuman peroxiredoxin-1 C83S mutant
ComponentsPeroxiredoxin-1
KeywordsOXIDOREDUCTASE / peroxiredoxin / C83S mutant / helix-to-loop conformational transition / CHAPS
Function / homology
Function and homology information


leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / natural killer cell mediated cytotoxicity / thioredoxin peroxidase activity / 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 / natural killer cell mediated cytotoxicity / thioredoxin peroxidase activity / 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 / RNA binding / extracellular space / extracellular exosome / identical protein binding / nucleus / 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: 2.1 Å
AuthorsCho, K.J. / Lee, J.-H. / Khan, T.G. / Park, Y. / Cho, A. / Chang, T.-S. / Kim, K.H.
CitationJournal: Bull.Korean Chem.Soc. / Year: 2015
Title: Crystal Structure of Dimeric Human Peroxiredoxin-1 C83S Mutant
Authors: Cho, K.J. / Park, Y. / Khan, T.G. / Lee, J.-H. / Kim, S. / Seok, J.H. / Chung, Y.B. / Cho, A.E. / Choi, Y. / Chang, T.-S. / Kim, K.H.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxiredoxin-1
B: Peroxiredoxin-1
C: Peroxiredoxin-1
D: Peroxiredoxin-1
E: Peroxiredoxin-1
F: Peroxiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,88912
Polymers145,7686
Non-polymers2,1216
Water7,188399
1
A: Peroxiredoxin-1
B: Peroxiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2964
Polymers48,5892
Non-polymers7072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-22 kcal/mol
Surface area15360 Å2
MethodPISA
2
C: Peroxiredoxin-1
D: Peroxiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2964
Polymers48,5892
Non-polymers7072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-22 kcal/mol
Surface area15310 Å2
MethodPISA
3
E: Peroxiredoxin-1
F: Peroxiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2964
Polymers48,5892
Non-polymers7072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-23 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.788, 80.128, 125.618
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number5
Space group name H-MC121

-
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


Mass: 24294.650 Da / Num. of mol.: 6 / Mutation: C83S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX1, PAGA, PAGB, TDPX2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q06830, peroxiredoxin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM imidazole, 0.8M potassium sodium tartrate, 200mM sodium chloride, pH 8.0, Temperature 295K
PH range: 7.5 - 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 79872 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Rsym value: 0.38 / Net I/σ(I): 31.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QQ2

1qq2


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.348 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 4013 5 %RANDOM
Rwork0.17551 ---
obs0.17793 75843 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.329 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å20.07 Å2
2--0.38 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8298 0 144 399 8841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198754
X-RAY DIFFRACTIONr_bond_other_d0.0010.028371
X-RAY DIFFRACTIONr_angle_refined_deg2.0361.97411898
X-RAY DIFFRACTIONr_angle_other_deg1.173319365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.47151084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66424.312385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.654151417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9371537
X-RAY DIFFRACTIONr_chiral_restr0.1820.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219811
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022003
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_it2.9773.0334291
X-RAY DIFFRACTIONr_mcbond_other2.973.0334290
X-RAY DIFFRACTIONr_mcangle_it3.9514.535363
X-RAY DIFFRACTIONr_mcangle_other3.9514.535364
X-RAY DIFFRACTIONr_scbond_it3.9363.4764463
X-RAY DIFFRACTIONr_scbond_other3.9363.4764464
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9825.0286527
X-RAY DIFFRACTIONr_long_range_B_refined7.57824.91510043
X-RAY DIFFRACTIONr_long_range_B_other7.57724.91610044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 299 -
Rwork0.22 5458 -
obs--97.16 %

+
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://pdbjlvh1.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