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- PDB-7c2b: Crystal structure of ferredoxin: thioredoxin reductase and thiore... -

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Basic information

Entry
Database: PDB / ID: 7c2b
TitleCrystal structure of ferredoxin: thioredoxin reductase and thioredoxin f2 complex
Components
  • (Ferredoxin-thioredoxin reductase ...) x 2
  • Thioredoxin F2, chloroplastic
KeywordsELECTRON TRANSPORT / FTR / Trx f2
Function / homology
Function and homology information


ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / response to light intensity / chloroplast envelope / plastid / chloroplast stroma / positive regulation of catalytic activity / enzyme activator activity / photosynthesis ...ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / response to light intensity / chloroplast envelope / plastid / chloroplast stroma / positive regulation of catalytic activity / enzyme activator activity / photosynthesis / cell redox homeostasis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / cytosol
Similarity search - Function
Ferredoxin thioredoxin reductase, alpha chain / Ferredoxin-thioredoxin reductase, variable chain / Ferredoxin thioredoxin reductase variable alpha chain / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Electron transport accessory-like domain superfamily / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. ...Ferredoxin thioredoxin reductase, alpha chain / Ferredoxin-thioredoxin reductase, variable chain / Ferredoxin thioredoxin reductase variable alpha chain / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Electron transport accessory-like domain superfamily / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
NITRATE ION / IRON/SULFUR CLUSTER / Ferredoxin-thioredoxin reductase subunit A2, chloroplastic / Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic / Thioredoxin F2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7949 Å
AuthorsKurisu, G. / Juniar, L. / Tanaka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H06560 Japan
CitationJournal: Protein Sci. / Year: 2020
Title: Structural basis for thioredoxin isoform-based fine-tuning of ferredoxin-thioredoxin reductase activity.
Authors: Juniar, L. / Tanaka, H. / Yoshida, K. / Hisabori, T. / Kurisu, G.
History
DepositionMay 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
B: Ferredoxin-thioredoxin reductase variable chain, chloroplastic
C: Thioredoxin F2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,68719
Polymers38,4433
Non-polymers1,24416
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-26 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.738, 83.943, 69.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Ferredoxin-thioredoxin reductase ... , 2 types, 2 molecules AB

#1: Protein Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic / FTR-C / Ferredoxin-thioredoxin reductase subunit B / FTR-B


Mass: 12995.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: Chloroplast / Gene: FTRC / Plasmid: pETDUET1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9SJ89, ferredoxin:thioredoxin reductase
#2: Protein Ferredoxin-thioredoxin reductase variable chain, chloroplastic / Ferredoxin/thioredoxin reductase subunit A (Variable subunit) 2 / Putative lipoic acid synthase


Mass: 12583.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: Chloroplast
Gene: FTRA2, ferredoxin, At5g08410, At5g08410/F8L15_140, C24_LOCUS21561, F8L15.14
Plasmid: pETDUET1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8LBP6

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Protein , 1 types, 1 molecules C

#3: Protein Thioredoxin F2, chloroplastic / AtTrxf2 / Thioredoxin F1 / AtTrxf1


Mass: 12863.915 Da / Num. of mol.: 1 / Mutation: C42S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: Chloroplast / Gene: At5g16400, MQK4.13 / Plasmid: pET23 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9XFH9

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Non-polymers , 4 types, 254 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 200 mM Mg Nitrate 16-20 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7949→48.7298 Å / Num. obs: 37811 / % possible obs: 99.43 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.08 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1045 / Rpim(I) all: 0.0431 / Rrim(I) all: 0.1132 / Net I/σ(I): 13.48
Reflection shellResolution: 1.7949→1.859 Å / Redundancy: 7 % / Rmerge(I) obs: 0.9917 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3690 / CC1/2: 0.809 / CC star: 0.946 / Rpim(I) all: 0.3983 / Rrim(I) all: 1.07 / % possible all: 98.48

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pu9

2pu9


Resolution: 1.7949→48.7298 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 20.21
RfactorNum. reflection% reflection
Rfree0.2105 1891 4.99 %
Rwork0.1793 --
obs0.1809 37802 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.81 Å2 / Biso mean: 28.3803 Å2 / Biso min: 14.45 Å2
Refinement stepCycle: final / Resolution: 1.7949→48.7298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 65 238 2773
Biso mean--35.04 33.94 -
Num. residues----310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7949-1.81850.2791390.2707252997
1.8185-1.84340.26091360.2571260699
1.8434-1.86980.25451410.2465262498
1.8698-1.89770.26341360.2426259499
1.8977-1.92730.25491400.2431261799
1.9273-1.95890.24071380.2249259199
1.9589-1.99270.29661360.2191261299
1.9927-2.0290.22471380.2192261199
2.029-2.0680.21221370.1995263799
2.068-2.11020.20971330.1851262699
2.1102-2.15610.18531390.1892260499
2.1561-2.20620.25171370.1853261399
2.2062-2.26140.25531380.1789261799
2.2614-2.32260.17441320.17552618100
2.3226-2.39090.19881360.176260399
2.3909-2.46810.21371410.18012650100
2.4681-2.55630.19991380.17792626100
2.5563-2.65860.20021370.18472643100
2.6586-2.77960.26211380.18382636100
2.7796-2.92610.2011390.18692627100
2.9261-3.10940.23311400.19032623100
3.1094-3.34950.20191420.17642605100
3.3495-3.68640.18721360.16132630100
3.6864-4.21960.17811300.14732651100
4.2196-5.31520.19661360.1458262899
5.3152-48.72980.18851400.1597260999

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