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- PDB-5nyl: Crystal structure of an atypical poplar thioredoxin-like2.1 activ... -

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Basic information

Entry
Database: PDB / ID: 5nyl
TitleCrystal structure of an atypical poplar thioredoxin-like2.1 active site mutant
ComponentsThioredoxin-like protein 2.1
KeywordsOXIDOREDUCTASE / atypical thioredoin / disulfide exchange
Function / homologyThioredoxin-like 3-1/3-2 / chloroplast stroma / Thioredoxin / 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: 1.5 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)28,1172
Polymers28,1172
Non-polymers00
Water4,035224
1
A: Thioredoxin-like protein 2.1


Theoretical massNumber of molelcules
Total (without water)14,0591
Polymers14,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin-like protein 2.1


Theoretical massNumber of molelcules
Total (without water)14,0591
Polymers14,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.650, 36.300, 100.150
Angle α, β, γ (deg.)90.00, 91.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thioredoxin-like protein 2.1


Mass: 14058.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus tremula x Populus tremuloides (plant)
Plasmid: pET3d / Details (production host): T7 expression strain / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I0BZV0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 1.86 Å3/Da / Density % sol: 33.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na3 citrate, 20%(w/v) 2-propanol, 20%(w/v) PEG 4K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→33.38 Å / Num. obs: 32801 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.039 / Net I/σ(I): 14.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2 / Num. unique obs: 1377 / CC1/2: 0.719 / Rpim(I) all: 0.41 / % possible all: 83.8

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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 atypical trx-like2.1

Resolution: 1.5→33.38 Å / Cor.coef. Fo:Fc: 0.9571 / Cor.coef. Fo:Fc free: 0.9434 / SU R Cruickshank DPI: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 999 3.05 %RANDOM
Rwork0.1784 ---
obs0.1794 32797 97.81 %-
Displacement parametersBiso mean: 20.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.6949 Å20 Å2-0.368 Å2
2---0.6925 Å20 Å2
3----1.0024 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: 1 / Resolution: 1.5→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 0 224 2084
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013777HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.076898HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d847SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes515HARMONIC5
X-RAY DIFFRACTIONt_it3777HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.94
X-RAY DIFFRACTIONt_other_torsion14.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion253SEMIHARMONIC5
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_contact4339SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.55 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2641 76 2.87 %
Rwork0.2183 2576 -
all0.2197 2652 -
obs--85.44 %

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