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- PDB-5nyo: Crystal structure of an atypical poplar thioredoxin-like2.1 varia... -

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Basic information

Entry
Database: PDB / ID: 5nyo
TitleCrystal structure of an atypical poplar thioredoxin-like2.1 variant in dimeric form
ComponentsThioredoxin-like protein 2.1
KeywordsOXIDOREDUCTASE / atypical thioredoxin / disulfide exchange / oxidoredutase
Function / homologyThioredoxin-like 3-1/3-2 / Thioredoxin / chloroplast stroma / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Thioredoxin-like protein 2.1
Function and homology information
Biological speciesPopulus tremula x Populus tremuloides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Thioredoxin-like protein 2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5094
Polymers28,3172
Non-polymers1922
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: covalently linked dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-28 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.547, 62.547, 138.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thioredoxin-like protein 2.1


Mass: 14158.645 Da / Num. of mol.: 2 / Mutation: C45S Engineered mutation
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium formate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.25→46.4 Å / Num. obs: 13773 / % possible obs: 100 % / Redundancy: 8.5 % / Biso Wilson estimate: 62.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Net I/σ(I): 14.9
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1242 / CC1/2: 0.745 / Rpim(I) all: 0.552 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wild-type Thioredoxin-like protein 2.1

Resolution: 2.25→46.4 Å / Cor.coef. Fo:Fc: 0.9518 / Cor.coef. Fo:Fc free: 0.9108 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.312 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.232
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 700 5.1 %RANDOM
Rwork0.2069 ---
obs0.2098 13714 99.99 %-
Displacement parametersBiso mean: 67.23 Å2
Baniso -1Baniso -2Baniso -3
1-4.4184 Å20 Å20 Å2
2--4.4184 Å20 Å2
3----8.8368 Å2
Refine analyzeLuzzati coordinate error obs: 0.318 Å
Refinement stepCycle: 1 / Resolution: 2.25→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 10 98 2046
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011992HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.122693HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d718SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes273HARMONIC5
X-RAY DIFFRACTIONt_it1992HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion18.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion261SEMIHARMONIC5
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_contact2329SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.43 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2598 147 5.35 %
Rwork0.2534 2601 -
all0.2538 2748 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.00011.0004-0.33684.7519-0.60782.17470.0132-0.0004-0.2873-0.1669-0.1885-0.29690.069-0.03540.1752-0.14680.0417-0.0163-0.0210.0128-0.037-15.3793-0.0718-13.8717
23.82680.369-0.46693.2182-1.02786.31890.0823-0.3131-0.00540.0302-0.06-0.0284-0.1050.3872-0.0223-0.1204-0.0478-0.0344-0.05130.038-0.1193-34.501312.41279.5434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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