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- PDB-6q47: Crystal structure of partially oxidized thioredoxin h1 from Chlam... -

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Basic information

Entry
Database: PDB / ID: 6q47
TitleCrystal structure of partially oxidized thioredoxin h1 from Chlamydomonas reinhardtii
ComponentsThioredoxin H-type
KeywordsELECTRON TRANSPORT / alfa/beta protein / thioredoxin fold / disulphide oxidoreductase / cell redox homeostatis
Function / homology
Function and homology information


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
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsFermani, S. / Zaffagnini, M. / Lemaire, S.D.
Funding support Italy, 1items
OrganizationGrant numberCountry
FARB2012-University of Bologna Italy
CitationJournal: Antioxidants (Basel) / Year: 2019
Title: Structural and Biochemical Insights into the Reactivity of Thioredoxin h1 fromChlamydomonas reinhardtii.
Authors: Marchand, C.H. / Fermani, S. / Rossi, J. / Gurrieri, L. / Tedesco, D. / Henri, J. / Sparla, F. / Trost, P. / Lemaire, S.D. / Zaffagnini, M.
History
DepositionDec 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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 H-type
B: Thioredoxin H-type


Theoretical massNumber of molelcules
Total (without water)23,7172
Polymers23,7172
Non-polymers00
Water3,099172
1
A: Thioredoxin H-type


Theoretical massNumber of molelcules
Total (without water)11,8591
Polymers11,8591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin H-type


Theoretical massNumber of molelcules
Total (without water)11,8591
Polymers11,8591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.683, 48.683, 143.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thioredoxin H-type / Trx-H / Thioredoxin-CH1


Mass: 11858.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cytoplasm / Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TRXH / Production host: Escherichia coli (E. coli) / References: UniProt: P80028
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10% (w/v) PEG 8K, 10% (w/v) PEG 10K, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2014 / Details: Silicon toroidal mirror coated with Rhodium
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→42.161 Å / Num. obs: 28348 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.034 / Net I/σ(I): 10
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2646 / CC1/2: 0.661 / Rpim(I) all: 0.428 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EPT

1ept


Resolution: 1.57→42.161 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.73
RfactorNum. reflection% reflection
Rfree0.2156 1350 4.77 %
Rwork0.1872 --
obs0.1886 28277 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.1 Å2
Refinement stepCycle: LAST / Resolution: 1.57→42.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 0 172 1810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061699
X-RAY DIFFRACTIONf_angle_d0.822315
X-RAY DIFFRACTIONf_dihedral_angle_d2.2591370
X-RAY DIFFRACTIONf_chiral_restr0.061273
X-RAY DIFFRACTIONf_plane_restr0.007292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5702-1.62630.27331320.26092539X-RAY DIFFRACTION96
1.6263-1.69140.22971270.22782662X-RAY DIFFRACTION100
1.6914-1.76840.25891210.2142666X-RAY DIFFRACTION100
1.7684-1.86160.2311390.21232659X-RAY DIFFRACTION100
1.8616-1.97820.25051380.19812667X-RAY DIFFRACTION100
1.9782-2.1310.24451370.1922684X-RAY DIFFRACTION100
2.131-2.34540.20411470.19172703X-RAY DIFFRACTION100
2.3454-2.68470.19281270.19522722X-RAY DIFFRACTION100
2.6847-3.38230.23031480.19942723X-RAY DIFFRACTION99
3.3823-42.17610.19621340.16122902X-RAY DIFFRACTION99

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