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- PDB-6i19: Crystal structure of Chlamydomonas reinhardtii thioredoxin h1 -

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Basic information

Entry
Database: PDB / ID: 6i19
TitleCrystal structure of Chlamydomonas reinhardtii thioredoxin h1
ComponentsThioredoxin H-type
KeywordsELECTRON TRANSPORT / h-type cytosolic thioredoxin oxidized
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: 1.378 Å
AuthorsLemaire, S.D. / Tedesco, D. / Crozet, P. / Michelet, L. / Fermani, S. / Zaffagnini, M. / Henri, J.
CitationJournal: Antioxidants (Basel) / Year: 2018
Title: Crystal Structure of Chloroplastic Thioredoxin f2 fromChlamydomonas reinhardtiiReveals Distinct Surface Properties.
Authors: Lemaire, S.D. / Tedesco, D. / Crozet, P. / Michelet, L. / Fermani, S. / Zaffagnini, M. / Henri, J.
History
DepositionOct 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: 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 9, 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
Water7,116395
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)48.760, 48.760, 143.970
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
11A-388-

HOH

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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.: 395 / 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: 40.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium sulfate, 100 mM sodium cacodylate, pH 6.5, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.378→36.42 Å / Num. obs: 41955 / % possible obs: 99.8 % / Redundancy: 2 % / Net I/σ(I): 25.45
Reflection shellResolution: 1.378→1.427 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ep7

1ep7


Resolution: 1.378→36.42 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.83
RfactorNum. reflection% reflection
Rfree0.2165 2095 4.99 %
Rwork0.1812 --
obs0.183 41953 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.378→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 0 395 2033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051672
X-RAY DIFFRACTIONf_angle_d0.7682272
X-RAY DIFFRACTIONf_dihedral_angle_d3.452581
X-RAY DIFFRACTIONf_chiral_restr0.084269
X-RAY DIFFRACTIONf_plane_restr0.005285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3776-1.40970.28491340.23532541X-RAY DIFFRACTION97
1.4097-1.44490.22651360.21012602X-RAY DIFFRACTION100
1.4449-1.4840.25171380.20892636X-RAY DIFFRACTION100
1.484-1.52770.20761370.20592616X-RAY DIFFRACTION100
1.5277-1.5770.25241390.20242641X-RAY DIFFRACTION100
1.577-1.63330.21381380.19532632X-RAY DIFFRACTION100
1.6333-1.69870.22821370.19062606X-RAY DIFFRACTION100
1.6987-1.77610.21371390.19652641X-RAY DIFFRACTION100
1.7761-1.86970.23361400.2022658X-RAY DIFFRACTION100
1.8697-1.98680.23531380.19142626X-RAY DIFFRACTION100
1.9868-2.14020.23281410.17932670X-RAY DIFFRACTION100
2.1402-2.35560.21911410.18572680X-RAY DIFFRACTION100
2.3556-2.69640.20441420.18332694X-RAY DIFFRACTION100
2.6964-3.39690.21451430.17452725X-RAY DIFFRACTION100
3.3969-40.53790.19951520.16072890X-RAY DIFFRACTION100

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