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- PDB-6i1c: Crystal structure of Chlamydomonas reinhardtii thioredoxin f2 -

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Basic information

Entry
Database: PDB / ID: 6i1c
TitleCrystal structure of Chlamydomonas reinhardtii thioredoxin f2
Componentsthioredoxin f2
KeywordsELECTRON TRANSPORT / f-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
Thioredoxin domain-containing protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLemaire, S.D. / Tedesco, D. / Crozet, P. / Michelet, L. / Fermani, S. / Zaffagnini, M. / Henri, J.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research Agency17-CE05-0001 France
French National Research AgencyANR-LABX-011 France
French National Research AgencyANR-11-EQPX-0008 France
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 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thioredoxin f2
B: thioredoxin f2
C: thioredoxin f2


Theoretical massNumber of molelcules
Total (without water)43,3103
Polymers43,3103
Non-polymers00
Water3,225179
1
A: thioredoxin f2


Theoretical massNumber of molelcules
Total (without water)14,4371
Polymers14,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: thioredoxin f2


Theoretical massNumber of molelcules
Total (without water)14,4371
Polymers14,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: thioredoxin f2


Theoretical massNumber of molelcules
Total (without water)14,4371
Polymers14,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.383, 97.475, 139.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

21A-260-

HOH

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Components

#1: Protein thioredoxin f2


Mass: 14436.664 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_05g243050v5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K3DSC9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES-NaOH, pH 7.5, 2% PEG 400, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.01→42.85 Å / Num. obs: 29702 / % possible obs: 98.74 % / Redundancy: 1.9 % / Net I/σ(I): 6.69
Reflection shellResolution: 2.01→2.082 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology modelling by PHYRE2

Resolution: 2.01→42.85 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.26
RfactorNum. reflection% reflection
Rfree0.2628 1998 6.72 %
Rwork0.2257 --
obs0.2282 29748 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.01→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 0 179 2764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082637
X-RAY DIFFRACTIONf_angle_d0.9683559
X-RAY DIFFRACTIONf_dihedral_angle_d2.7971606
X-RAY DIFFRACTIONf_chiral_restr0.057403
X-RAY DIFFRACTIONf_plane_restr0.007443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.06030.32111440.31351992X-RAY DIFFRACTION100
2.0603-2.1160.38581400.30521970X-RAY DIFFRACTION100
2.116-2.17830.3041430.30771975X-RAY DIFFRACTION99
2.1783-2.24860.29321380.26941914X-RAY DIFFRACTION98
2.2486-2.32890.30711440.27112008X-RAY DIFFRACTION100
2.3289-2.42220.30011420.25121951X-RAY DIFFRACTION99
2.4222-2.53240.27091430.24711984X-RAY DIFFRACTION100
2.5324-2.66590.34371420.24471977X-RAY DIFFRACTION99
2.6659-2.83290.30891400.25561958X-RAY DIFFRACTION98
2.8329-3.05160.2821430.25141981X-RAY DIFFRACTION99
3.0516-3.35870.25191440.21881992X-RAY DIFFRACTION99
3.3587-3.84450.24861410.19711971X-RAY DIFFRACTION97
3.8445-4.8430.2111450.17052005X-RAY DIFFRACTION98
4.843-48.75180.23431490.2212072X-RAY DIFFRACTION97

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