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Yorodumi- PDB-1fa6: CRYSTAL STRUCTURE OF THE CO(II)-BOUND GLYOXALASE I OF ESCHERICHIA COLI -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fa6 | ||||||
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Title | CRYSTAL STRUCTURE OF THE CO(II)-BOUND GLYOXALASE I OF ESCHERICHIA COLI | ||||||
Components | GLYOXALASE I | ||||||
Keywords | LYASE / Beta-Alpha-Beta-Beta-Beta motif / homodimer / protein-Co(II) complex | ||||||
Function / homology | Function and homology information lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / nickel cation binding / response to toxic substance / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 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 | 1fa6.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fa6.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fa6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fa6_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 1fa6_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 1fa6_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1fa6_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/1fa6 ftp://data.pdbj.org/pub/pdb/validation_reports/fa/1fa6 | HTTPS FTP |
-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 one 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: Chemical | #3: 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: 39.41 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 5 Details: PEG 1000, PEG 8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 12, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 17383 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.11 / % possible all: 88.7 |
Reflection | *PLUS Num. measured all: 116932 |
Reflection shell | *PLUS % possible obs: 88.7 % / Mean I/σ(I) obs: 6.1 |
-Processing
Software |
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Refinement | Resolution: 1.9→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: 0.74 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor all: 0.18 / Rfactor obs: 0.169 / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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