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- PDB-8ys1: Crystal structure of rat thioredoxin, Wild-type -

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Basic information

Entry
Database: PDB / ID: 8ys1
TitleCrystal structure of rat thioredoxin, Wild-type
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: 2.112 Å
AuthorsBaba, T. / Ueno, G. / Ohe, C. / Saji, S. / Yamamoto, S. / Yamamoto, M. / Ouchida, M. / Kawasaki-Ohmori, I. / Takeshita, K.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)27,6352
Polymers27,6352
Non-polymers00
Water1,838102
1
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)13,8181
Polymers13,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)13,8181
Polymers13,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.640, 74.300, 53.950
Angle α, β, γ (deg.)90.000, 101.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thioredoxin / Trx


Mass: 13817.690 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Txn, Txn1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11232
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 15–16% PEG-3350, 9% glycerol, and 0.1 M citric acid (pH 3.5)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / 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: 2.11→50 Å / Num. obs: 13638 / % possible obs: 99.5 % / Redundancy: 3.75 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.113 / Net I/σ(I): 14.07
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.11-2.240.67222040.7550.7871
2.24-2.390.46320050.8440.5421
2.39-2.50.38511800.8840.451
2.5-30.20134570.9630.2341
3-40.0627450.9970.071
4-60.02614290.9990.031
6-500.0261810.0241

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OO5

4oo5


Resolution: 2.112→43.057 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.856 / SU ML: 0.146 / Cross valid method: FREE R-VALUE / ESU R: 0.209 / ESU R Free: 0.181
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2299 682 5.001 %
Rwork0.1818 12955 -
all0.184 --
obs-13637 99.81 %
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: 29.754 Å2
Baniso -1Baniso -2Baniso -3
1--0.997 Å2-0 Å2-0.113 Å2
2---0.344 Å2-0 Å2
3---1.279 Å2
Refinement stepCycle: LAST / Resolution: 2.112→43.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 0 102 1730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121660
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161560
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.6292236
X-RAY DIFFRACTIONr_angle_other_deg0.4661.5753628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.045208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45110296
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.4071072
X-RAY DIFFRACTIONr_chiral_restr0.0620.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
X-RAY DIFFRACTIONr_nbd_refined0.2320.2306
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.21362
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2826
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.293
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.217
X-RAY DIFFRACTIONr_nbd_other0.2260.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.27
X-RAY DIFFRACTIONr_mcbond_it2.5812.866838
X-RAY DIFFRACTIONr_mcbond_other2.5812.866838
X-RAY DIFFRACTIONr_mcangle_it3.855.1421044
X-RAY DIFFRACTIONr_mcangle_other3.8485.1421045
X-RAY DIFFRACTIONr_scbond_it3.8473.276822
X-RAY DIFFRACTIONr_scbond_other3.8453.275823
X-RAY DIFFRACTIONr_scangle_it5.975.7891192
X-RAY DIFFRACTIONr_scangle_other5.9675.7881193
X-RAY DIFFRACTIONr_lrange_it7.76733.2851856
X-RAY DIFFRACTIONr_lrange_other7.76733.0791845
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
2.112-2.1670.323500.289620.28210170.9150.94299.50840.261
2.167-2.2260.287490.2649280.2669770.9440.9511000.233
2.226-2.290.267470.2438810.2449300.9460.96199.78490.212
2.29-2.3610.314480.2419150.2449640.9380.96199.89630.213
2.361-2.4380.288430.2448180.2468610.9470.9621000.216
2.438-2.5230.272440.2098360.2128800.9570.9721000.178
2.523-2.6180.245410.1947810.1968230.9670.97799.87850.155
2.618-2.7240.243400.1917660.1948070.9610.97799.87610.158
2.724-2.8450.257390.1847360.1877780.9670.97899.61440.15
2.845-2.9830.203370.1737070.1757440.9740.9811000.141
2.983-3.1440.197350.1546560.1566920.9790.98599.85550.131
3.144-3.3330.22330.1516420.1556780.9750.98699.55750.13
3.333-3.5620.264320.1575910.1626250.9690.98599.680.139
3.562-3.8450.215300.1645690.1676000.9780.98499.83330.148
3.845-4.2090.187260.1565030.1585290.9810.9841000.143
4.209-4.70.237240.1364560.1414820.9740.98999.58510.129
4.7-5.4160.177220.164160.1614390.9860.98699.77220.148
5.416-6.6070.182190.1833540.1833730.9770.9811000.16
6.607-9.2360.202140.1582720.1612880.9760.98699.30560.151
9.236-43.0570.10490.1841660.181750.9910.9841000.216

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