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- PDB-2oe0: Crystal Structure of Mitochondrial Thioredoxin 3 from Saccharomyc... -

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Basic information

Entry
Database: PDB / ID: 2oe0
TitleCrystal Structure of Mitochondrial Thioredoxin 3 from Saccharomyces cerevisiae
ComponentsThioredoxin-3
KeywordsELECTRON TRANSPORT / alpha/beta sandwich / dimer
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / The NLRP3 inflammasome / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / Oxidative Stress Induced Senescence / cellular response to oxidative stress / mitochondrion
Similarity search - Function
: / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-3, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBao, R. / Zhang, Y.R. / Zhou, C.Z. / Chen, Y.X.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Structural and mechanistic analyses of yeast mitochondrial thioredoxin Trx3 reveal putative function of its additional cysteine residues
Authors: Bao, R. / Zhang, Y.R. / Zhou, C.-Z. / Chen, Y.X.
History
DepositionDec 27, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 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-3
B: Thioredoxin-3


Theoretical massNumber of molelcules
Total (without water)25,7382
Polymers25,7382
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.569, 49.569, 94.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Thioredoxin-3


Mass: 12868.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: TRX3 / Plasmid: pET28a(modified) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25372
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M sodium acetate, 8% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2→25.38 Å / Num. obs: 17467 / % possible obs: 99.66 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 3.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERU

1eru


Resolution: 2→25.38 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19986 882 5.1 %RANDOM
Rwork0.17266 ---
obs0.1741 16573 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.811 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 0 170 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221687
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9912284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4645210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12425.93864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24515318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.192154
X-RAY DIFFRACTIONr_chiral_restr0.1010.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021220
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.2776
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21135
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2711.51060
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07721730
X-RAY DIFFRACTIONr_scbond_it1.6683627
X-RAY DIFFRACTIONr_scangle_it2.5084.5554
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 65 -
Rwork0.187 1227 -
obs--98.7 %

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