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Open data
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Basic information
Entry | Database: PDB / ID: 7vq6 | ||||||
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Title | Structure of a specialized glyoxalase from Gossypium hirsutum | ||||||
![]() | Lactoylglutathione lyase | ||||||
![]() | LYASE / glyoxalase | ||||||
Function / homology | ![]() lactoylglutathione lyase / lactoylglutathione lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Li, H. / Hu, Y.M. / Dai, L.H. / Chen, C.C. / Huang, J.W. / Liu, W.D. / Guo, R.T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure and biochemical analysis of the specialized deoxynivalenol-detoxifying glyoxalase SPG from Gossypium hirsutum. Authors: Hu, Y. / Li, H. / Min, J. / Yu, Y. / Liu, W. / Huang, J.W. / Zhang, L. / Yang, Y. / Dai, L. / Chen, C.C. / Guo, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.5 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qipS 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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Unit cell |
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Components
#1: Protein | Mass: 21293.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: MgAC; Sodium Cacodylate ; PEG 4000. |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Sep 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→44.48 Å / Num. obs: 66039 / % possible obs: 99.8 % / Redundancy: 6.85 % / Rmerge(I) obs: 0.0809 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.39→1.49 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 2731 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QIP Resolution: 1.39→44.48 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.636 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.012 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 62.72 Å2 / Biso mean: 13.291 Å2 / Biso min: 4.52 Å2
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Refinement step | Cycle: final / Resolution: 1.39→44.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.39→1.426 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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