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- PDB-6q6u: Crystal structure of C39S mutant of thioredoxin h1 from Chlamydom... -

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Basic information

Entry
Database: PDB / ID: 6q6u
TitleCrystal structure of C39S 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, 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: 1.81 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


Theoretical massNumber of molelcules
Total (without water)23,6852
Polymers23,6852
Non-polymers00
Water2,918162
1
A: Thioredoxin H-type


Theoretical massNumber of molelcules
Total (without water)11,8431
Polymers11,8431
Non-polymers00
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)48.431, 48.431, 143.659
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-264-

HOH

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Components

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


Mass: 11842.665 Da / Num. of mol.: 2 / Mutation: C39S
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 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: ELETTRA / Beamline: 5.2R / 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: 1.81→41.94 Å / Num. obs: 18676 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.057 / Rrim(I) all: 0.133 / Net I/σ(I): 9.7
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1044 / CC1/2: 0.715 / Rpim(I) all: 0.345 / Rrim(I) all: 0.891 / % possible all: 97

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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: 1.81→41.94 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 28.13
RfactorNum. reflection% reflection
Rfree0.2663 1786 5.25 %
Rwork0.2191 --
obs0.2216 18626 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 1.81→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 0 162 1794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021670
X-RAY DIFFRACTIONf_angle_d0.4382269
X-RAY DIFFRACTIONf_dihedral_angle_d1.8171173
X-RAY DIFFRACTIONf_chiral_restr0.045270
X-RAY DIFFRACTIONf_plane_restr0.003284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.85430.45241380.34832443X-RAY DIFFRACTION97
1.8543-1.90890.36971120.29372501X-RAY DIFFRACTION99
1.9089-1.97050.31361400.28112496X-RAY DIFFRACTION98
1.9705-2.04090.2722970.25442494X-RAY DIFFRACTION98
2.0409-2.12270.35341290.25312513X-RAY DIFFRACTION99
2.1227-2.21930.32041250.2552587X-RAY DIFFRACTION100
2.2193-2.33620.31951510.24422451X-RAY DIFFRACTION100
2.3362-2.48260.29251840.25112455X-RAY DIFFRACTION99
2.4826-2.67430.36411480.24862468X-RAY DIFFRACTION98
2.6743-2.94330.29771310.24142427X-RAY DIFFRACTION97
2.9433-3.36910.2391930.21732425X-RAY DIFFRACTION98
3.3691-4.2440.19561160.17952514X-RAY DIFFRACTION98
4.244-41.940.18511220.15692490X-RAY DIFFRACTION98

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