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Yorodumi- PDB-1qh5: HUMAN GLYOXALASE II WITH S-(N-HYDROXY-N-BROMOPHENYLCARBAMOYL)GLUT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qh5 | ||||||
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Title | HUMAN GLYOXALASE II WITH S-(N-HYDROXY-N-BROMOPHENYLCARBAMOYL)GLUTATHIONE | ||||||
Components | PROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE) | ||||||
Keywords | HYDROLASE / METALLO-HYDROLASE | ||||||
Function / homology | Function and homology information hydroxyacylglutathione hydrolase / hydroxyacylglutathione hydrolase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / glutathione biosynthetic process / Pyruvate metabolism / glutathione metabolic process / mitochondrial matrix / mitochondrion / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.45 Å | ||||||
Authors | Cameron, A.D. / Ridderstrom, M. / Olin, B. / Mannervik, B. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Crystal structure of human glyoxalase II and its complex with a glutathione thiolester substrate analogue. Authors: Cameron, A.D. / Ridderstrom, M. / Olin, B. / Mannervik, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qh5.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qh5.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/1qh5 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/1qh5 | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99987, -0.01367, 0.00851), Vector: |
-Components
#1: Protein | Mass: 28904.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Description: HETEROLOGOUSLY EXPRESSED / Plasmid: PKK 223-3,ACCI-DELETED / Production host: Escherichia coli (E. coli) / Strain (production host): JM 109 References: UniProt: Q16775, hydroxyacylglutathione hydrolase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GSH / | #4: Chemical | ChemComp-GBP / | #5: 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: 32 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: EQUILABRATION AGAINST 4-20% W/V PEG 2000 MONOMETHYL ETHER, pH 6.5 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.1 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-4 / Wavelength: 0.9317 |
Detector | Type: ADSC / Detector: CCD / Date: Nov 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9317 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→43 Å / Num. obs: 437671 / % possible obs: 99 % / Redundancy: 5.2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4 / % possible all: 100 |
Reflection | *PLUS Num. obs: 84815 / Num. measured all: 437671 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.45→20 Å / SU B: 1.3 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08
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Displacement parameters | Biso mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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