+Open data
-Basic information
Entry | Database: PDB / ID: 7wt2 | ||||||
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Title | human glyoxalase I in complex with TLSC702 | ||||||
Components | Lactoylglutathione lyase | ||||||
Keywords | LYASE / glyoxalase I / zinc metalloenzyme | ||||||
Function / homology | Function and homology information lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding ...lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Usami, M. / Yokoyama, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Febs Lett. / Year: 2022 Title: Crystal structures of human glyoxalase I and its complex with TLSC702 reveal inhibitor binding mode and substrate preference. Authors: Usami, M. / Ando, K. / Shibuya, A. / Takasawa, R. / Yokoyama, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wt2.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wt2.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 7wt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wt2_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7wt2_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7wt2_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 7wt2_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/7wt2 ftp://data.pdbj.org/pub/pdb/validation_reports/wt/7wt2 | HTTPS FTP |
-Related structure data
Related structure data | 7wszC 7wt0C 7wt1C 3vw9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 1 - 183 / Label seq-ID: 2 - 184
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-Components
#1: Protein | Mass: 20803.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04760, lactoylglutathione lyase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.41 Å3/Da / Density % sol: 48.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 0.1 M Bis-Tris, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 25974 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 4 / Num. unique obs: 3727 / CC1/2: 0.96 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3vw9 Resolution: 2→19.81 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.78 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.174 / 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: 119.43 Å2 / Biso mean: 36.571 Å2 / Biso min: 20.2 Å2
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Refinement step | Cycle: final / Resolution: 2→19.81 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 5633 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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