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- PDB-6q6v: Crystal structure (trigonal form) of C36S mutant of thioredoxin h... -

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Basic information

Entry
Database: PDB / ID: 6q6v
TitleCrystal structure (trigonal form) of C36S mutant of thioredoxin h1 from Chlamydomonas reinhardtii
ComponentsThioredoxin H-type
KeywordsELECTRON TRANSPORT / alpha/beta protein / thioredoxin fold / disulphide oxidoreductase / cell redox homeostatis
Function / homology
Function and homology information


Thioredoxin / Thioredoxin family active site. / Thioredoxin, conserved site / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Thioredoxin H-type
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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 11, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7913
Polymers23,6852
Non-polymers1061
Water6,233346
1
A: Thioredoxin H-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9492
Polymers11,8431
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin H-type


Theoretical massNumber of molelcules
Total (without water)11,8431
Polymers11,8431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.742, 48.742, 143.187
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: 11842.665 Da / Num. of mol.: 2 / Mutation: C36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TRXH / Organ: cytoplasm / Production host: Escherichia coli (E. coli) / References: UniProt: P80028
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% (w/v) PEG 8K, 10% (w/v) PEG 10K, 0.1 M HEPES

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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 S 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: 1.22→42.21 Å / Num. obs: 59565 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 12.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 14.7
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2934 / CC1/2: 0.635 / Rpim(I) all: 0.507 / Rrim(I) all: 1.311 / % possible all: 98.7

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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: 1EP7

1ep7


Resolution: 1.22→42.21 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 20
RfactorNum. reflection% reflection
Rfree0.1743 5738 5.09 %
Rwork0.1682 --
obs0.1685 59506 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.2 Å2
Refinement stepCycle: LAST / Resolution: 1.22→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 7 346 2001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071710
X-RAY DIFFRACTIONf_angle_d1.0792325
X-RAY DIFFRACTIONf_dihedral_angle_d15.727605
X-RAY DIFFRACTIONf_chiral_restr0.085276
X-RAY DIFFRACTIONf_plane_restr0.007292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.23390.27711400.29663457X-RAY DIFFRACTION98
1.2339-1.24840.30122080.29043534X-RAY DIFFRACTION98
1.2484-1.26360.30141420.2933571X-RAY DIFFRACTION98
1.2636-1.27960.31482060.28543542X-RAY DIFFRACTION99
1.2796-1.29640.25771840.2663512X-RAY DIFFRACTION99
1.2964-1.31420.28971900.26443573X-RAY DIFFRACTION99
1.3142-1.3330.26112330.26093495X-RAY DIFFRACTION99
1.333-1.35290.27272210.2573571X-RAY DIFFRACTION99
1.3529-1.3740.27511260.24113600X-RAY DIFFRACTION99
1.374-1.39660.23861640.23053627X-RAY DIFFRACTION100
1.3966-1.42060.24361820.22093523X-RAY DIFFRACTION100
1.4206-1.44650.20961990.20563578X-RAY DIFFRACTION99
1.4465-1.47430.20851720.21213615X-RAY DIFFRACTION100
1.4743-1.50440.2061960.19853559X-RAY DIFFRACTION100
1.5044-1.53710.22741800.18983587X-RAY DIFFRACTION100
1.5371-1.57290.18151750.18313642X-RAY DIFFRACTION100
1.5729-1.61220.19031780.17913533X-RAY DIFFRACTION100
1.6122-1.65580.19811700.16893606X-RAY DIFFRACTION100
1.6558-1.70450.20671600.16753606X-RAY DIFFRACTION100
1.7045-1.75950.19122160.16473549X-RAY DIFFRACTION100
1.7595-1.82240.18052100.16363546X-RAY DIFFRACTION100
1.8224-1.89540.14181880.16273607X-RAY DIFFRACTION100
1.8954-1.98160.17931840.15193581X-RAY DIFFRACTION100
1.9816-2.08610.14272020.14723583X-RAY DIFFRACTION100
2.0861-2.21680.17291900.14563626X-RAY DIFFRACTION100
2.2168-2.3880.14422580.13813468X-RAY DIFFRACTION100
2.388-2.62820.15812250.14713552X-RAY DIFFRACTION100
2.6282-3.00840.17042180.15133581X-RAY DIFFRACTION100
3.0084-3.790.14492060.14553570X-RAY DIFFRACTION100
3.79-42.2370.14552150.14663548X-RAY DIFFRACTION100

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