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Yorodumi- PDB-6lyw: Structural insight into the biological functions of Arabidopsis t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lyw | ||||||
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Title | Structural insight into the biological functions of Arabidopsis thaliana ACHT1 | ||||||
Components | Thioredoxin-like 2-1, chloroplastic | ||||||
Keywords | STRUCTURAL PROTEIN / Arabidopsis thaliana / 2-Cys PrxA / Peroxidase activity. | ||||||
Function / homology | Function and homology information regulation of photosynthesis / detection of redox state / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / chloroplast stroma / chloroplast / cell redox homeostasis Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wang, J.C. / Pan, W.M. / Wang, M.Z. / Zhang, M. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2020 Title: Structural insight into the biological functions of Arabidopsis thaliana ACHT1. Authors: Wang, J. / Pan, W. / Cai, W. / Wang, M. / Liu, L. / Zhang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lyw.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lyw.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 6lyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/6lyw ftp://data.pdbj.org/pub/pdb/validation_reports/ly/6lyw | HTTPS FTP |
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-Related structure data
Related structure data | 6lyxC 3zzxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17226.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g26160, F20B18.270 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8LEK4 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: ammonium sulfate, isopropanol,agarose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: LIQUID ANODE / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. obs: 52610 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 14.07 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.031 / Rrim(I) all: 0.072 / Χ2: 0.913 / Net I/σ(I): 9.7 / Num. measured all: 253890 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3zzx Resolution: 1.7→32.403 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.94 Å2 / Biso mean: 18.8 Å2 / Biso min: 6.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→32.403 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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