+Open data
-Basic information
Entry | Database: PDB / ID: 7vq6 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a specialized glyoxalase from Gossypium hirsutum | ||||||
Components | Lactoylglutathione lyase | ||||||
Keywords | LYASE / glyoxalase | ||||||
Function / homology | Function and homology information lactoylglutathione lyase / lactoylglutathione lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Gossypium hirsutum (cotton) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||
Authors | Li, H. / Hu, Y.M. / Dai, L.H. / Chen, C.C. / Huang, J.W. / Liu, W.D. / Guo, R.T. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7vq6.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vq6.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vq6_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7vq6_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7vq6_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 7vq6_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/7vq6 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/7vq6 | HTTPS FTP |
-Related structure data
Related structure data | 1qipS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21293.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gossypium hirsutum (cotton) / Gene: LOC107963917 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1U8Q028, lactoylglutathione lyase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.04 % |
---|---|
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 |
---|---|
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.39→44.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.39→1.426 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|