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

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Basic information

Entry
Database: PDB / ID: 7bzk
TitleCrystal structure of ferredoxin: thioredoxin reductase and thioredoxin y1 complex
Components
  • Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
  • Thioredoxin Y1, chloroplastic
KeywordsELECTRON TRANSPORT / FTR / Trx y1
Function / homology
Function and homology information


ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / positive regulation of catalytic activity / chloroplast envelope / chloroplast stroma / protein-disulfide reductase activity / chloroplast / enzyme activator activity / 4 iron, 4 sulfur cluster binding ...ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / positive regulation of catalytic activity / chloroplast envelope / chloroplast stroma / protein-disulfide reductase activity / chloroplast / enzyme activator activity / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Thioredoxin Y1, chloroplastic / Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5935 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
DepositionApr 28, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
B: Thioredoxin Y1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9493
Polymers25,5972
Non-polymers3521
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-35 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.985, 60.762, 61.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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 Thioredoxin Y1, chloroplastic / AtTrxy1


Mass: 12601.493 Da / Num. of mol.: 1 / Mutation: C34S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: chloroplast / Gene: At1g76760, F28O16.13 / Plasmid: pET23 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6NPF9
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 100 mM Magnesium Citric acid pH 3.5 5% 2-propanol 5-9% PEG 3,350
PH range: 3.5-7.5

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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: 1.5935→43.0845 Å / Num. obs: 27925 / % possible obs: 99.89 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1197 / Rpim(I) all: 0.05048 / Rrim(I) all: 0.1301 / Net I/σ(I): 10.4
Reflection shellResolution: 1.5935→1.651 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.7606 / Num. unique obs: 2737 / CC1/2: 0.861 / CC star: 0.962 / Rpim(I) all: 0.3309 / Rrim(I) all: 0.8309 / % possible all: 99.56

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PU9

2pu9


Resolution: 1.5935→43.0845 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.54
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1397 5 %1397
Rwork0.17 26528 --
obs0.171 27925 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.41 Å2 / Biso mean: 22.45 Å2 / Biso min: 8.97 Å2
Refinement stepCycle: final / Resolution: 1.5935→43.0845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 8 108 1821
Biso mean--12.7 29.77 -
Num. residues----214
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5935-1.65050.26711360.2358258599
1.6505-1.71660.26441370.19712592100
1.7166-1.79470.21051390.17522645100
1.7947-1.88930.20021370.16872597100
1.8893-2.00770.19961380.16412627100
2.0077-2.16270.18921400.15842654100
2.1627-2.38030.20021390.16572643100
2.3803-2.72470.20761400.1722665100
2.7247-3.43270.1971420.17632707100
3.4327-43.08450.15711490.15832813100

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