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- PDB-7rhp: Crystal Structure of Honeybee (Apis mellifera) glutathione S-tran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rhp | ||||||
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Title | Crystal Structure of Honeybee (Apis mellifera) glutathione S-transferase AmGSTD1 | ||||||
![]() | Glutathione S-transferase AmGSTD1 | ||||||
![]() | TRANSFERASE / glutathione s-transferase / GSH / delta / honeybee / Apis mellifera / complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
Model details | complex with GSH | ||||||
![]() | Moural, T.W. / Zhu, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Architecture and potential roles of a delta-class glutathione S-transferase in protecting honey bee from agrochemicals. Authors: Moural, T.W. / Koirala B K, S. / Bhattarai, G. / He, Z. / Guo, H. / Phan, N.T. / Rajotte, E.G. / Biddinger, D.J. / Hoover, K. / Zhu, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.2 KB | Display | ![]() |
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PDB format | ![]() | 77.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 780.7 KB | Display | ![]() |
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Full document | ![]() | 782.6 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wywS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29331.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GSH / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.34 % |
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Crystal grow | Temperature: 291 K / Method: evaporation Details: 0.2 M Sodium chloride, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→52.04 Å / Num. obs: 37014 / % possible obs: 95 % / Redundancy: 16.9 % / Biso Wilson estimate: 21.58 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07798 / Rpim(I) all: 0.01925 / Rrim(I) all: 0.08041 / Net I/σ(I): 14.34 |
Reflection shell | Resolution: 1.54→1.595 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.9732 / Mean I/σ(I) obs: 0.34 / Num. unique obs: 2976 / CC1/2: 0.772 / CC star: 0.933 / Rpim(I) all: 0.2854 / % possible all: 73.91 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WYW Resolution: 1.54→52.04 Å / SU ML: 0.1617 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.5595 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→52.04 Å
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Refine LS restraints |
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LS refinement shell |
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