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- PDB-6q6t: Crystal structure (orthorombic form) of C36S mutant of thioredoxi... -

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Basic information

Entry
Database: PDB / ID: 6q6t
TitleCrystal structure (orthorombic form) of C36S mutant of 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
DI(HYDROXYETHYL)ETHER / Thioredoxin H-type
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2675
Polymers11,8431
Non-polymers4244
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint9 kcal/mol
Surface area5940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.777, 34.815, 48.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

21A-366-

HOH

31A-440-

HOH

41A-467-

HOH

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Components

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


Mass: 11842.665 Da / Num. of mol.: 1 / 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.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% (w/v) PEG 10K, 0.1 M sodium cacodylate

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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: 0.94→48.16 Å / Num. obs: 64505 / % possible obs: 96.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 8.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.033 / Rrim(I) all: 0.054 / Net I/σ(I): 18.9
Reflection shellResolution: 0.94→0.96 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1579 / CC1/2: 0.625 / Rpim(I) all: 0.367 / Rrim(I) all: 0.52 / % possible all: 47.1

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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: 0.94→48.158 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 15.77
RfactorNum. reflection% reflection
Rfree0.1655 5883 4.95 %
Rwork0.1574 --
obs0.1578 64420 92.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 12.6 Å2
Refinement stepCycle: LAST / Resolution: 0.94→48.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 28 207 1049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006872
X-RAY DIFFRACTIONf_angle_d1.0071177
X-RAY DIFFRACTIONf_dihedral_angle_d12.846316
X-RAY DIFFRACTIONf_chiral_restr0.081137
X-RAY DIFFRACTIONf_plane_restr0.007146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.95070.3346610.2872981X-RAY DIFFRACTION24
0.9507-0.96190.2681300.2922188X-RAY DIFFRACTION54
0.9619-0.97360.25711390.24612965X-RAY DIFFRACTION72
0.9736-0.98590.23542020.23563358X-RAY DIFFRACTION84
0.9859-0.99890.21942110.22123813X-RAY DIFFRACTION94
0.9989-1.01260.21052380.20743958X-RAY DIFFRACTION99
1.0126-1.02710.20352010.19494087X-RAY DIFFRACTION99
1.0271-1.04240.18061990.19663951X-RAY DIFFRACTION98
1.0424-1.05870.16441960.19183952X-RAY DIFFRACTION97
1.0587-1.0760.19622250.18173930X-RAY DIFFRACTION97
1.076-1.09460.2012220.17384001X-RAY DIFFRACTION99
1.0946-1.11450.18592270.16764001X-RAY DIFFRACTION99
1.1145-1.13590.16921800.16263998X-RAY DIFFRACTION98
1.1359-1.15910.17832060.16194043X-RAY DIFFRACTION98
1.1591-1.18430.13461870.1643943X-RAY DIFFRACTION96
1.1843-1.21190.17462480.16153986X-RAY DIFFRACTION99
1.2119-1.24220.14121930.16134047X-RAY DIFFRACTION99
1.2422-1.27580.16941810.15814023X-RAY DIFFRACTION99
1.2758-1.31330.16542320.15654017X-RAY DIFFRACTION99
1.3133-1.35570.17332510.15643989X-RAY DIFFRACTION99
1.3557-1.40420.16231930.15413980X-RAY DIFFRACTION97
1.4042-1.46040.17291950.15394041X-RAY DIFFRACTION99
1.4604-1.52690.1652330.14873976X-RAY DIFFRACTION99
1.5269-1.60740.16931770.14534054X-RAY DIFFRACTION99
1.6074-1.70810.13481830.14114004X-RAY DIFFRACTION98
1.7081-1.840.15032220.14633917X-RAY DIFFRACTION96
1.84-2.02510.13511920.1443922X-RAY DIFFRACTION96
2.0251-2.31820.14921750.14084027X-RAY DIFFRACTION98
2.3182-2.92060.14551760.14873984X-RAY DIFFRACTION97
2.9206-48.22130.17682080.1573788X-RAY DIFFRACTION93

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