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- PDB-7ysi: Crystal structure of thioredoxin 2 -

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Basic information

Entry
Database: PDB / ID: 7ysi
TitleCrystal structure of thioredoxin 2
ComponentsThiol disulfide reductase thioredoxin
KeywordsOXIDOREDUCTASE / Trx2 / thioredoxin2
Function / homology
Function and homology information


protein-disulfide reductase / protein-disulfide reductase activity / metal ion binding / cytosol
Similarity search - Function
: / Thioredoxin 2, N-terminal / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Thiol disulfide reductase thioredoxin
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.202 Å
AuthorsChang, Y.J. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Iucrj / Year: 2023
Title: Comparison of the structure and activity of thioredoxin 2 and thioredoxin 1 from Acinetobacter baumannii.
Authors: Chang, Y.J. / Sung, J.H. / Lee, C.S. / Lee, J.H. / Park, H.H.
History
DepositionAug 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol disulfide reductase thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8673
Polymers16,7361
Non-polymers1312
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-17 kcal/mol
Surface area7630 Å2
Unit cell
Length a, b, c (Å)34.590, 55.010, 78.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thiol disulfide reductase thioredoxin / Thioredoxin / Thioredoxin 2 / Thioredoxin TrxC


Mass: 16736.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: trxC, AYR68_15440, B7L45_02985, BAA1790NC_0521, BS065_02615, CBL15_02595, CTZ19_02595, D8O08_003970, DLI71_14475, DLI72_02635, E2532_03525, E2533_03310, E2534_07555, E2535_02615, E2536_10370, ...Gene: trxC, AYR68_15440, B7L45_02985, BAA1790NC_0521, BS065_02615, CBL15_02595, CTZ19_02595, D8O08_003970, DLI71_14475, DLI72_02635, E2532_03525, E2533_03310, E2534_07555, E2535_02615, E2536_10370, E2538_07040, E2539_06760, E2540_11860, E2541_06480, EA720_013275, FDN00_17805, FE003_02610, IAG11_14015
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A219CD23
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES/NaOH pH 7.0, 15% PEG 20000

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.202→27.42 Å / Num. obs: 45597 / % possible obs: 96.64 % / Redundancy: 12.7 % / Biso Wilson estimate: 14.86 Å2 / Rmerge(I) obs: 0.09366 / Net I/σ(I): 15.42
Reflection shellResolution: 1.202→27.42 Å / Rmerge(I) obs: 2.435 / Num. unique obs: 4106

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3p2a

3p2a


Resolution: 1.202→27.418 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 2280 5 %
Rwork0.1749 43303 -
obs0.1755 45583 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.49 Å2 / Biso mean: 19.4527 Å2 / Biso min: 9.91 Å2
Refinement stepCycle: final / Resolution: 1.202→27.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 0 2 217 1341
Biso mean--12.35 26.92 -
Num. residues----143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.202-1.22810.41771240.4786235485
1.2281-1.25660.42551360.4115259895
1.2566-1.28810.33371390.3201263596
1.2881-1.32290.29641400.2568266196
1.3229-1.36180.2141400.2206265097
1.3618-1.40580.24151430.2043271097
1.4058-1.4560.18641400.195265997
1.456-1.51430.21531420.2012271097
1.5143-1.58320.17691420.1685268797
1.5832-1.66670.16021430.1638272998
1.6667-1.77110.17221440.1594273698
1.7711-1.90780.16641460.1604277498
1.9078-2.09970.17741460.1614276599
2.0997-2.40340.16041480.1523281799
2.4034-3.02740.2011490.1647282099
3.0274-27.4180.16881580.15772998100

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