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Yorodumi- PDB-1fa8: CRYSTAL STRUCTURE OF THE APO FORM GLYOXALASE I OF ESCHERICHIA COLI -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fa8 | ||||||
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Title | CRYSTAL STRUCTURE OF THE APO FORM GLYOXALASE I OF ESCHERICHIA COLI | ||||||
Components | GLYOXALASE ILactoylglutathione lyase | ||||||
Keywords | LYASE / Beta-alpha-Beta-Beta-Beta motif / homodimer / apo enzyme. | ||||||
Function / homology | Function and homology information lactoylglutathione lyase / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / lactoylglutathione lyase activity / nickel cation binding / response to toxic substance / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | He, M.M. / Clugston, S.L. / Honek, J.F. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation. Authors: He, M.M. / Clugston, S.L. / Honek, J.F. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fa8.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fa8.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fa8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/1fa8 ftp://data.pdbj.org/pub/pdb/validation_reports/fa/1fa8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a homodimer in each asymmetric unit and the two monomers are related by non-crystallographic symmetry. |
-Components
#1: Protein | Mass: 14936.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC81, lactoylglutathione lyase #2: 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: 2.07 Å3/Da / Density % sol: 40.65 % | ||||||||||||||||||||
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Crystal grow | Temperature: 275 K / pH: 5 Details: PEG 1000, PEG 4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 275K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.78 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 29051 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.24 / % possible all: 93.1 |
Reflection | *PLUS Num. measured all: 81372 |
Reflection shell | *PLUS % possible obs: 93.1 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Resolution: 1.7→20 Å / Isotropic thermal model: TNT BCORREL VERSION 1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO VERSION 1.0
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.68 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor all: 0.19 / Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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