+Open data
-Basic information
Entry | Database: PDB / ID: 5a5k | ||||||
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Title | AtGSTF2 from Arabidopsis thaliana in complex with camalexin | ||||||
Components | GLUTATHIONE S-TRANSFERASE F2 | ||||||
Keywords | TRANSFERASE / GLUTATHIONE-S-TRANSFERASE / GST / PLANT / ARABIDOPSIS | ||||||
Function / homology | Function and homology information response to oomycetes / camalexin binding / quercitrin binding / salicylic acid binding / toxin catabolic process / auxin-activated signaling pathway / glutathione binding / plasmodesma / plant-type vacuole / apoplast ...response to oomycetes / camalexin binding / quercitrin binding / salicylic acid binding / toxin catabolic process / auxin-activated signaling pathway / glutathione binding / plasmodesma / plant-type vacuole / apoplast / chloroplast stroma / response to zinc ion / glutathione transferase / glutathione transferase activity / response to cadmium ion / response to cold / glutathione metabolic process / chloroplast / defense response / peroxidase activity / protein domain specific binding / intracellular membrane-bounded organelle / endoplasmic reticulum / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Ahmad, L. / Rylott, E. / Bruce, N.C. / Edwards, R. / Grogan, G. | ||||||
Citation | Journal: FEBS Open Bio / Year: 2017 Title: Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands. Authors: Ahmad, L. / Rylott, E.L. / Bruce, N.C. / Edwards, R. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a5k.cif.gz | 942.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a5k.ent.gz | 780.5 KB | Display | PDB format |
PDBx/mmJSON format | 5a5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a5k_validation.pdf.gz | 633.8 KB | Display | wwPDB validaton report |
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Full document | 5a5k_full_validation.pdf.gz | 767.3 KB | Display | |
Data in XML | 5a5k_validation.xml.gz | 185.3 KB | Display | |
Data in CIF | 5a5k_validation.cif.gz | 228.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/5a5k ftp://data.pdbj.org/pub/pdb/validation_reports/a5/5a5k | HTTPS FTP |
-Related structure data
Related structure data | 5a4uC 5a4vC 5a4wC 1gnwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 24162.566 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: P46422, glutathione transferase #2: Chemical | ChemComp-7WB / ( #3: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.2 M SODIUM ACETATE AND 20% (W/V) PEG 3350; PH 7.0; PROTEIN AT 10 MG PER ML |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→87.58 Å / Num. obs: 126932 / % possible obs: 98.6 % / Observed criterion σ(I): 1.8 / Redundancy: 2.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.77→2.84 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.8 / % possible all: 98.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GNW Resolution: 2.77→87.58 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / SU B: 20.734 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.77→87.58 Å
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Refine LS restraints |
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