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- PDB-7bzk: Crystal structure of ferredoxin: thioredoxin reductase and thiore... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bzk | ||||||
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Title | Crystal structure of ferredoxin: thioredoxin reductase and thioredoxin y1 complex | ||||||
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![]() | ELECTRON TRANSPORT / FTR / Trx y1 | ||||||
Function / homology | ![]() ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / oxidoreductase activity, acting on iron-sulfur proteins as donors / glycerol ether metabolic process / protein-disulfide reductase (NAD(P)H) activity / chloroplast envelope / chloroplast stroma / positive regulation of catalytic activity / protein-disulfide reductase activity ...ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / oxidoreductase activity, acting on iron-sulfur proteins as donors / glycerol ether metabolic process / protein-disulfide reductase (NAD(P)H) activity / chloroplast envelope / chloroplast stroma / positive regulation of catalytic activity / protein-disulfide reductase activity / enzyme activator activity / chloroplast / cell redox homeostasis / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kurisu, G. / Juniar, L. / Tanaka, H. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60 KB | Display | ![]() |
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PDB format | ![]() | 41.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7c2bC ![]() 7c3fC ![]() 7c65C ![]() 2pu9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12995.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9SJ89, ferredoxin:thioredoxin reductase |
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#2: Protein | Mass: 12601.493 Da / Num. of mol.: 1 / Mutation: C34S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-SF4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 2PU9 Resolution: 1.5935→43.0845 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.41 Å2 / Biso mean: 22.45 Å2 / Biso min: 8.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5935→43.0845 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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