+Open data
-Basic information
Entry | Database: PDB / ID: 1bh5 | ||||||
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Title | HUMAN GLYOXALASE I Q33E, E172Q DOUBLE MUTANT | ||||||
Components | LACTOYLGLUTATHIONE LYASE | ||||||
Keywords | LYASE / 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 / 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 / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Cameron, A.D. / Jones, T.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Involvement of an active-site Zn2+ ligand in the catalytic mechanism of human glyoxalase I. Authors: Ridderstrom, M. / Cameron, A.D. / Jones, T.A. / Mannervik, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bh5.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bh5.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bh5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1bh5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1bh5_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 1bh5_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/1bh5 ftp://data.pdbj.org/pub/pdb/validation_reports/bh/1bh5 | HTTPS FTP |
-Related structure data
Related structure data | 1froS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE BIOLOGICALLY ACTIVE MOLECULE IS THE DIMER (MOLECULES A AND B OR C AND D). THE TWO DIMERS IN THE ASYMMETRIC UNIT ARE SITUATED IN SIMILAR CRYSTALLOGRAHIC ENVIRONMENTS. DURING REFINEMENT NON-CRYSTALLOGRAPHIC RESTRAINTS WERE APPLIED BETWEEN THE A AND C MOLECULES AND BETWEEN THE B AND D MOLECULES). NO NCS RESTRAINTS WERE APPLIED BETWEEN THE TWO MOLECULES OF THE DIMERS. DISORDERED SIDE CHAINS HAVE BEEN INCLUDED WITH OCCUPANCIES OF 0.01. RESIDUE CYS 60 IN THE B AND D MOLECULES APPEARS TO BE INVOLVED IN A DISULFIDE BRIDGE WITH 2-MERCAPTOETHANOL AS STATED FOR 1FRO.PDB. THE 2-MERCAPTOETHANOL HAS NOT BEEN MODELLED DUE TO THE LIMITED NUMBER OF DATA. |
-Components
#1: Protein | Mass: 20672.520 Da / Num. of mol.: 4 / Mutation: Q33E, E172Q 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-GTX / #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 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 Details: PROTEIN WAS CRYSTALLISED FROM PEG 2000 MONOMETHLY ETHER 50 MM MES PH 5.8, 0.1M NACL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / Details: Cameron, A.D., (1997) EMBO J., 16, 3386. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 23, 1997 |
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: 33195 / % possible obs: 89.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 5.5 / % possible all: 63.1 |
Reflection shell | *PLUS % possible obs: 63 % |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB ENTRY 1FRO Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.25 / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |