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- PDB-6g62: Crystal structure of thioredoxin O2 from Arabidopsis thaliana in ... -

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Basic information

Entry
Database: PDB / ID: 6g62
TitleCrystal structure of thioredoxin O2 from Arabidopsis thaliana in oxidized state
ComponentsThioredoxin O2, mitochondrial
KeywordsOXIDOREDUCTASE / Thioredoxin
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / mitochondrion
Similarity search - Function
: / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin O2, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsRoret, T. / Didierjean, C.
CitationJournal: Antioxidants (Basel) / Year: 2018
Title: MitochondrialArabidopsis thalianaTRXo Isoforms Bind an Iron−Sulfur Cluster and Reduce NFU Proteins In Vitro.
Authors: Zannini, F. / Roret, T. / Przybyla-Toscano, J. / Dhalleine, T. / Rouhier, N. / Couturier, J.
History
DepositionMar 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin O2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)14,5221
Polymers14,5221
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.806, 70.806, 35.755
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Thioredoxin O2, mitochondrial / AtTrxo2


Mass: 14521.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g31020, F17F8.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93VQ9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.78 Å3/Da / Density % sol: 30.97 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 100 mM citrate buffer (pH 5.6) 30% PEG 4000 100 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9815 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9815 Å / Relative weight: 1
ReflectionResolution: 1.5→35.403 Å / Num. obs: 16473 / % possible obs: 99.4 % / Redundancy: 12 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.028 / Rrim(I) all: 0.075 / Net I/σ(I): 20
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 814 / CC1/2: 0.942 / Rpim(I) all: 0.251 / Rrim(I) all: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2722: ???)refinement
XDSdata reduction
Aimlessdata scaling
ARP/wARPmodel building
Cootmodel building
MolProbitymodel building
RefinementResolution: 1.5→35.403 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.41
RfactorNum. reflection% reflection
Rfree0.1793 766 4.65 %
Rwork0.1674 --
obs0.168 16458 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→35.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms884 0 0 92 976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003902
X-RAY DIFFRACTIONf_angle_d0.5281220
X-RAY DIFFRACTIONf_dihedral_angle_d10.941548
X-RAY DIFFRACTIONf_chiral_restr0.046141
X-RAY DIFFRACTIONf_plane_restr0.003153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.6160.18621290.19223131X-RAY DIFFRACTION99
1.616-1.77860.23981450.19293092X-RAY DIFFRACTION99
1.7786-2.0360.19821590.17753120X-RAY DIFFRACTION99
2.036-2.5650.19561490.16893154X-RAY DIFFRACTION100
2.565-35.41310.16211840.15823195X-RAY DIFFRACTION100
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)
13.76560.26021.3321.6319-0.01820.4806-0.0383-0.4317-0.6823-0.2958-0.1512-0.31580.47710.1775-0.47810.21720.01980.04510.17710.04430.30725.8877-15.70784.9279
20.96670.6703-0.46960.88-0.69992.2434-0.34840.4941-0.1407-0.42980.2650.01060.4572-0.0141-0.0410.3122-0.03490.02470.2457-0.02520.201222.8183-10.0888-4.7518
30.47-0.34610.40390.277-0.24220.43020.34880.0116-0.23370.1245-0.2082-0.0276-0.13490.1290.00050.2413-0.0036-0.01980.28860.00480.206530.4617-4.63618.2766
41.1470.4314-0.23790.7214-0.16010.5154-0.1021-0.1881-0.5633-0.0004-0.1354-0.14780.12140.1292-0.16980.1727-0.00090.03470.12780.02910.174724.9125-9.98191.9751
52.31882.4006-0.81455.0828-1.70220.5715-0.03041.2039-0.7198-1.2757-0.5101-0.5480.47540.6915-0.04520.8693-0.2310.04760.9673-0.02830.374827.1757-7.5582-12.1664
60.5342-0.10970.52610.33770.20880.7815-0.17430.49990.4199-0.24380.19950.22720.0694-0.13550.01470.2043-0.0392-0.02710.22490.05520.185922.7053-1.5828-3.8396
70.6357-0.0436-0.57953.1117-0.79891.155-0.0446-0.11220.18980.1936-0.03360.1214-0.0365-0.0892-0.00050.1815-0.0054-0.01710.18960.01470.169719.72791.86594.449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 76 )
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 90 )
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 113 )

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