+Open data
-Basic information
Entry | Database: PDB / ID: 1fro | ||||||
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Title | HUMAN GLYOXALASE I WITH BENZYL-GLUTATHIONE INHIBITOR | ||||||
Components | LACTOYLGLUTATHIONE LYASE | ||||||
Keywords | LACTOYLGLUTATHIONE LYASE / GLYOXALASE I | ||||||
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 / extracellular exosome ...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 / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.2 Å | ||||||
Authors | Cameron, A.D. / Jones, T.A. | ||||||
Citation | Journal: EMBO J. / Year: 1997 Title: Crystal structure of human glyoxalase I--evidence for gene duplication and 3D domain swapping. Authors: Cameron, A.D. / Olin, B. / Ridderstrom, M. / Mannervik, B. / Jones, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fro.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fro.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/1fro ftp://data.pdbj.org/pub/pdb/validation_reports/fr/1fro | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 20672.520 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04760, lactoylglutathione lyase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GSB / #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: 2.37 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 / Details: pH 5.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 20, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 35503 / % possible obs: 91.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3 / % possible all: 78.1 |
Reflection | *PLUS Num. measured all: 118633 |
Reflection shell | *PLUS % possible obs: 79.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→7.5 Å / Isotropic thermal model: RESTRAINED INDIVIDUAL Details: THIS STRUCTURE WAS REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS BETWEEN ALL MOLECULES. WATER MOLECULES B 246 AND B 253 ARE INVOLVED IN STEREOCHEMICAL CLASHES ON GENERATION ...Details: THIS STRUCTURE WAS REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS BETWEEN ALL MOLECULES. WATER MOLECULES B 246 AND B 253 ARE INVOLVED IN STEREOCHEMICAL CLASHES ON GENERATION OF THE FULL ASYMMETRIC UNIT. DISORDERED SIDE CHAINS HAVE BEEN INCLUDED WITH OCCUPANCIES OF 0.01. THE DENSITY ASSOCIATED WITH THE LAST THREE RESIDUES IS RATHER POOR AND CONSEQUENTLY THE POSITIONS OF THESE RESIDUES ARE RATHER AMBIGUOUS.
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Displacement parameters | Biso mean: 23.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT NCS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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