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- PDB-7d6l: Crystal structure of Trx2 from D. radiodurans R1 -

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Basic information

Entry
Database: PDB / ID: 7d6l
TitleCrystal structure of Trx2 from D. radiodurans R1
ComponentsThioredoxin 2
KeywordsOXIDOREDUCTASE / antioxidant / thioredoxin / redox control / cysteine thiol-disulfide exchange
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / metal ion binding / 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 speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.947 Å
AuthorsKim, M.-K. / Zhang, J. / Zhao, L.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1F1A1057780 Korea, Republic Of
CitationJournal: Antioxidants / Year: 2021
Title: Structural and Biochemical Characterization of Thioredoxin-2 from Deinococcus radiodurans.
Authors: Kim, M.-K. / Zhao, L. / Jeong, S. / Zhang, J. / Jung, J.-H. / Seo, H.S. / Choi, J.- / Lim, S.
History
DepositionSep 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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: Thioredoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4492
Polymers16,3841
Non-polymers651
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7560 Å2
Unit cell
Length a, b, c (Å)101.887, 57.819, 36.152
Angle α, β, γ (deg.)90.000, 94.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thioredoxin 2 / Trx2


Mass: 16383.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / Gene: DR_A0164 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RYY9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal growTemperature: 295 K / Method: microbatch / Details: PEG 3350, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.947→50 Å / Num. obs: 14566 / % possible obs: 94.9 % / Redundancy: 5.1 % / CC1/2: 0.993 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Net I/σ(I): 50.779
Reflection shellResolution: 1.947→1.99 Å / Mean I/σ(I) obs: 11.628 / Num. unique obs: 685 / CC1/2: 0.971 / Rpim(I) all: 0.118 / Rrim(I) all: 0.262

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1v98

1v98


Resolution: 1.947→18.935 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 1453 10 %
Rwork0.1911 13073 -
obs0.1947 14526 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.28 Å2 / Biso mean: 38.3938 Å2 / Biso min: 13.57 Å2
Refinement stepCycle: final / Resolution: 1.947→18.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 1 74 1162
Biso mean--25.68 48.57 -
Num. residues----142
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.947-2.01620.28761350.2263123088
2.0162-2.09680.33391450.2369128994
2.0968-2.19210.22591550.1987136299
2.1921-2.30750.30291260.2197113983
2.3075-2.45170.2151580.1843138699
2.4517-2.64060.24681630.19061374100
2.6406-2.90550.25231390.20691377100
2.9055-3.32390.20771390.19191407100
3.3239-4.18040.22161380.1685120987
4.1804-18.9350.19071550.184130092
Refinement TLS params.Method: refined / Origin x: 35.221 Å / Origin y: 50.7825 Å / Origin z: 6.1787 Å
111213212223313233
T0.1436 Å2-0.0062 Å20.0084 Å2-0.154 Å2-0.017 Å2--0.1672 Å2
L1.3291 °2-0.5564 °20.8443 °2-1.1786 °2-0.3234 °2--1.9199 °2
S0.0246 Å °-0.1532 Å °-0.0219 Å °-0.0462 Å °0.0361 Å °-0.0736 Å °0.0437 Å °-0.1221 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 142
2X-RAY DIFFRACTION1allA201
3X-RAY DIFFRACTION1allS1 - 74

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