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Yorodumi- PDB-4pv5: Crystal structure of mouse glyoxalase I in complexed with 18-beta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pv5 | ||||||
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Title | Crystal structure of mouse glyoxalase I in complexed with 18-beta-glycyrrhetinic acid | ||||||
Components | Lactoylglutathione lyase | ||||||
Keywords | LYASE/LYASE INHIBITOR / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Pyruvate metabolism / lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding ...Pyruvate metabolism / lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhang, H. / Zhai, J. / Zhang, L.P. / Zhao, Y.N. / Li, C. / Hu, X.P. | ||||||
Citation | Journal: Acta Pharmacol.Sin. / Year: 2015 Title: Structural basis for 18-beta-glycyrrhetinic acid as a novel non-GSH analog glyoxalase I inhibitor Authors: Zhang, H. / Huang, Q. / Zhai, J. / Zhao, Y.N. / Zhang, L.P. / Chen, Y.Y. / Zhang, R.W. / Li, Q. / Hu, X.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pv5.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pv5.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pv5_validation.pdf.gz | 750.2 KB | Display | wwPDB validaton report |
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Full document | 4pv5_full_validation.pdf.gz | 753.1 KB | Display | |
Data in XML | 4pv5_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 4pv5_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/4pv5 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/4pv5 | HTTPS FTP |
-Related structure data
Related structure data | 2za0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20704.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Glo1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(+) / References: UniProt: Q9CPU0, lactoylglutathione lyase #2: Chemical | #3: Chemical | ChemComp-CBW / ( | #4: 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: 2.03 Å3/Da / Density % sol: 39.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 30% PEG 2000, 50mM MES, 0.1M NaCl, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å | ||||||||||||
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Sep 18, 2013 | ||||||||||||
Radiation | Monochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 2.2→25.86 Å / Num. obs: 16786 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | ||||||||||||
Reflection shell |
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-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZA0 Resolution: 2.3→22.258 Å / FOM work R set: 0.8248 / SU ML: 0.31 / σ(F): 1.36 / Phase error: 24.75 / Stereochemistry target values: ML
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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 max: 93.09 Å2 / Biso mean: 27.33 Å2 / Biso min: 7.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→22.258 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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