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- PDB-5nyn: Crystal structure of the atypical poplar thioredoxin-like2.1 in c... -

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Basic information

Entry
Database: PDB / ID: 5nyn
TitleCrystal structure of the atypical poplar thioredoxin-like2.1 in complex with gluathione
ComponentsThioredoxin-like protein 2.1
KeywordsOXIDOREDUCTASE / atypical thioredoxin / disulfide exchange
Function / homologyThioredoxin-like 3-1/3-2 / chloroplast stroma / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / GLUTATHIONE / Thioredoxin-like protein 2.1
Function and homology information
Biological speciesPopulus tremula x Populus tremuloides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChibani, K. / Saul, F.A. / Haouz, A. / Rouhier, N.
Funding support France, 2items
OrganizationGrant numberCountry
INRA-FORMAS program France
Institut Pasteur France
CitationJournal: FEBS Lett. / Year: 2018
Title: Structural snapshots along the reaction mechanism of the atypical poplar thioredoxin-like2.1.
Authors: Chibani, K. / Saul, F. / Didierjean, C. / Rouhier, N. / Haouz, A.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-like protein 2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5943
Polymers14,1911
Non-polymers4032
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-12 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.708, 52.146, 59.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thioredoxin-like protein 2.1


Mass: 14190.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus tremula x Populus tremuloides (plant)
Plasmid: pET3d / Details (production host): T7 expression system / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I0BZV0
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na acetate, 0.2M lithium sulfate, 0.1M hepes7.5, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.6→46.7 Å / Num. obs: 19810 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.039 / Net I/σ(I): 15.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2 / Num. unique obs: 984 / CC1/2: 0.694 / Rpim(I) all: 0.548 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→16.4 Å / Cor.coef. Fo:Fc: 0.9572 / Cor.coef. Fo:Fc free: 0.9372 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.075
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 1017 5.21 %RANDOM
Rwork0.1646 ---
obs0.1659 19506 98.26 %-
Displacement parametersBiso mean: 23.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.6047 Å20 Å20 Å2
2---4.594 Å20 Å2
3---2.9893 Å2
Refine analyzeLuzzati coordinate error obs: 0.182 Å
Refinement stepCycle: 1 / Resolution: 1.6→16.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 19 165 1188
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012090HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063811HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d475SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes25HARMONIC2
X-RAY DIFFRACTIONt_gen_planes294HARMONIC5
X-RAY DIFFRACTIONt_it2090HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.23
X-RAY DIFFRACTIONt_other_torsion13.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion134SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2281SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2183 155 5.93 %
Rwork0.1917 2459 -
all0.1934 2614 -
obs--91.62 %

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