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- PDB-6q46: Crystal structure of reduced thioredoxin h1 from Chlamydomonas re... -

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Basic information

Entry
Database: PDB / ID: 6q46
TitleCrystal structure of reduced 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: 1.7 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

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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
Water3,459192
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
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
Unit cell
Length a, b, c (Å)48.769, 48.769, 143.930
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
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.: 192 / 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: 298 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: 1.7→47.98 Å / Num. obs: 22494 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 25.8 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.064 / Net I/σ(I): 7.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2165 / CC1/2: 0.683 / Rpim(I) all: 0.398 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EP7

1ep7


Resolution: 1.7→42.235 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.28
RfactorNum. reflection% reflection
Rfree0.224 1083 4.82 %
Rwork0.1888 --
obs0.1906 22475 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 0 192 1840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061712
X-RAY DIFFRACTIONf_angle_d0.7432332
X-RAY DIFFRACTIONf_dihedral_angle_d2.5051198
X-RAY DIFFRACTIONf_chiral_restr0.059276
X-RAY DIFFRACTIONf_plane_restr0.005295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.77740.28451600.26332564X-RAY DIFFRACTION98
1.7774-1.87110.29311110.24442651X-RAY DIFFRACTION98
1.8711-1.98830.25641030.20832618X-RAY DIFFRACTION99
1.9883-2.14180.25791190.20752676X-RAY DIFFRACTION99
2.1418-2.35740.23331430.19972631X-RAY DIFFRACTION99
2.3574-2.69840.25591380.20632686X-RAY DIFFRACTION99
2.6984-3.39950.23911710.19592694X-RAY DIFFRACTION100
3.3995-42.2480.17631380.15682872X-RAY DIFFRACTION99

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