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- PDB-5nyk: Crystal structure of the atypical poplar thioredoxin-like2.1 in o... -

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Basic information

Entry
Database: PDB / ID: 5nyk
TitleCrystal structure of the atypical poplar thioredoxin-like2.1 in oxidized state
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 / : / PHOSPHATE ION / Thioredoxin-like protein 2.1
Function and homology information
Biological speciesPopulus tremula x Populus tremuloides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)14,4555
Polymers14,1911
Non-polymers2644
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-16 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.697, 52.863, 59.083
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 strain / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I0BZV0
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.4M NaH2PO4, 1.6M K2PO4, 0.2M NaCl, imidazole

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.05→39.4 Å / Num. obs: 66294 / % possible obs: 95.6 % / Redundancy: 13.5 % / Biso Wilson estimate: 8.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.28 / Net I/σ(I): 19.4
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3045 / CC1/2: 0.883 / Rpim(I) all: 0.295 / % possible all: 89.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EP7

1ep7


Resolution: 1.05→15.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.9673 / SU R Cruickshank DPI: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.028 / SU Rfree Blow DPI: 0.028 / SU Rfree Cruickshank DPI: 0.024
RfactorNum. reflection% reflectionSelection details
Rfree0.1622 3295 5.05 %RANDOM
Rwork0.1547 ---
obs0.155 65284 94.74 %-
Displacement parametersBiso mean: 13.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.9653 Å20 Å20 Å2
2---0.6446 Å20 Å2
3---1.6099 Å2
Refine analyzeLuzzati coordinate error obs: 0.107 Å
Refinement stepCycle: LAST / Resolution: 1.05→15.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 12 300 1269
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012019HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.053697HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d459SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes24HARMONIC2
X-RAY DIFFRACTIONt_gen_planes275HARMONIC5
X-RAY DIFFRACTIONt_it2019HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.66
X-RAY DIFFRACTIONt_other_torsion12.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion133SEMIHARMONIC5
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_contact2397SEMIHARMONIC4
LS refinement shellResolution: 1.05→1.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1998 224 5.41 %
Rwork0.1922 3917 -
all0.1926 4141 -
obs--81.85 %

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