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- PDB-2oe1: Crystal Structure of Mitochondrial Thioredoxin 3 from Saccharomyc... -

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Basic information

Entry
Database: PDB / ID: 2oe1
TitleCrystal Structure of Mitochondrial Thioredoxin 3 from Saccharomyces cerevisiae (reduced form)
ComponentsThioredoxin-3
KeywordsELECTRON TRANSPORT / alpha/beta sandwich / reduced / dimer
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / The NLRP3 inflammasome / Detoxification of Reactive Oxygen Species / disulfide oxidoreductase activity / 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: 2.1 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 28, 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 ...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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin-3
B: Thioredoxin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0265
Polymers25,7382
Non-polymers2883
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-47 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.575, 49.575, 94.554
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: -1 - 104 / Label seq-ID: 9 - 114

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
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, 8mM DTT, 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 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.1→25.41 Å / Num. obs: 14192 / % possible obs: 93.5 % / Biso Wilson estimate: 19.05 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.4
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2040 / % possible all: 91.9

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Processing

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

1eru


Resolution: 2.1→25.41 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.915 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 724 5.1 %RANDOM
Rwork0.15954 ---
obs0.16258 13460 93.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.653 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.1 Å20 Å2
2---0.21 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 15 180 1851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221698
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9992300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12225.93864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6615318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.05154
X-RAY DIFFRACTIONr_chiral_restr0.0960.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021220
X-RAY DIFFRACTIONr_nbd_refined0.1940.2772
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.210
X-RAY DIFFRACTIONr_mcbond_it1.24321090
X-RAY DIFFRACTIONr_mcangle_it1.9631730
X-RAY DIFFRACTIONr_scbond_it1.572681
X-RAY DIFFRACTIONr_scangle_it2.4313570
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 828 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.430.5
medium thermal1.152
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 54 -
Rwork0.182 1004 -
obs--91.92 %

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