[English] 日本語
Yorodumi
- PDB-8ys3: Crystal structure of rat thioredoxin, F54L mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ys3
TitleCrystal structure of rat thioredoxin, F54L mutant
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


Protein repair / Interconversion of nucleotide di- and triphosphates / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / cellular response to hyperoxia / TP53 Regulates Metabolic Genes / Oxidative Stress Induced Senescence / cellular detoxification of hydrogen peroxide / protein-disulfide reductase [NAD(P)H] activity / response to selenium ion ...Protein repair / Interconversion of nucleotide di- and triphosphates / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / cellular response to hyperoxia / TP53 Regulates Metabolic Genes / Oxidative Stress Induced Senescence / cellular detoxification of hydrogen peroxide / protein-disulfide reductase [NAD(P)H] activity / response to selenium ion / response to thyroxine / thioredoxin-disulfide reductase (NADPH) activity / negative regulation of protein export from nucleus / positive regulation of DNA binding / cellular response to antibiotic / response to nitric oxide / response to dexamethasone / protein-disulfide reductase activity / response to axon injury / cell redox homeostasis / response to activity / cellular response to glucose stimulus / response to radiation / cellular response to xenobiotic stimulus / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / axon / neuronal cell body / dendrite / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsTakeshita, K. / Baba, T. / Ohe, C. / Saji, S. / Yamamoto, S. / Yamamoto, M. / Ouchida, M. / Kawasaki-Ohmori, I.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2025
Title: The F54L mutation of Thioredoxin shows protein instability and increased fluctuations of the catalytic center.
Authors: Baba, T. / Ueno, G. / Ohe, C. / Saji, S. / Yamamoto, S. / Yamamoto, M. / Nakagawa, H. / Okazaki, N. / Ouchida, M. / Ohmori, I.K. / Takeshita, K.
History
DepositionMar 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)27,5672
Polymers27,5672
Non-polymers00
Water2,288127
1
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)13,7841
Polymers13,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)13,7841
Polymers13,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.210, 33.350, 67.090
Angle α, β, γ (deg.)90.000, 107.740, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Thioredoxin / Trx


Mass: 13783.674 Da / Num. of mol.: 2 / Mutation: F54L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Txn, Txn1 / Details (production host): pET-22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P11232
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 3 M NaCl and 0.1 M citric acid (pH 3.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2022
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.752→50 Å / Num. obs: 20302 / % possible obs: 99.8 % / Redundancy: 4.06 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.047 / Net I/σ(I): 21.95
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.86-1.990.36930810.9040.4261
1.99-20.2591920.9370.2991
2-2.50.11666520.990.1341
2.5-30.0529510.9980.0581
3-40.02523540.9990.0291
4-60.01712430.9990.021
6-500.01755010.021

-
Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD0

3kd0


Resolution: 1.752→44.965 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.17 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1016 5.004 %RANDOM
Rwork0.1897 19286 --
all0.192 ---
obs-20302 99.852 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.669 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.762 Å2
2---1.257 Å2-0 Å2
3---0.125 Å2
Refinement stepCycle: LAST / Resolution: 1.752→44.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 0 127 1749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121652
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161564
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6292226
X-RAY DIFFRACTIONr_angle_other_deg0.4831.5753638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4885208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53210298
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.9771070
X-RAY DIFFRACTIONr_chiral_restr0.0730.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_nbd_refined0.2290.2311
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21360
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2802
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.269
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2790.228
X-RAY DIFFRACTIONr_nbd_other0.2010.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2660.216
X-RAY DIFFRACTIONr_mcbond_it2.7032.754838
X-RAY DIFFRACTIONr_mcbond_other2.7012.753838
X-RAY DIFFRACTIONr_mcangle_it3.7124.9411044
X-RAY DIFFRACTIONr_mcangle_other3.7214.9421045
X-RAY DIFFRACTIONr_scbond_it4.3613.214814
X-RAY DIFFRACTIONr_scbond_other4.3583.214815
X-RAY DIFFRACTIONr_scangle_it6.585.6571182
X-RAY DIFFRACTIONr_scangle_other6.5775.6561183
X-RAY DIFFRACTIONr_lrange_it8.05834.2331831
X-RAY DIFFRACTIONr_lrange_other8.01433.7121818
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.752-1.7980.319730.30613730.30614520.9290.93599.58680.287
1.798-1.8470.316730.26313950.26614690.9290.95399.93190.232
1.847-1.90.26690.24213110.24313810.9550.9699.92760.212
1.9-1.9590.284700.22813200.2313900.9450.9651000.196
1.959-2.0230.256660.21812570.2213230.9610.9681000.188
2.023-2.0940.256650.20712440.2113100.9580.97199.92370.175
2.094-2.1730.271620.19811670.20212300.9550.97499.91870.174
2.173-2.2610.225600.19111460.19312060.970.9771000.172
2.261-2.3610.255570.210860.20311430.9630.9761000.174
2.361-2.4760.263550.19310450.19711010.9550.97799.90920.169
2.476-2.610.235520.1999930.20110470.9650.97699.8090.181
2.61-2.7680.237510.1779610.1810150.9710.98199.70440.162
2.768-2.9580.195460.2018780.2019270.9720.97299.67640.185
2.958-3.1940.219440.1948300.1958760.9720.97699.77170.187
3.194-3.4970.191400.1837520.1847930.970.98199.87390.185
3.497-3.9070.218370.1667070.1687450.9650.98299.86580.179
3.907-4.5050.172320.1426230.1436550.9820.9881000.157
4.505-5.5040.179280.175300.1715610.9840.98499.46520.194
5.504-7.7260.246220.1814180.1844400.9620.9811000.201
7.726-44.9650.333140.182490.1862660.8980.97998.87220.228

+
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