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Yorodumi- PDB-1qip: HUMAN GLYOXALASE I COMPLEXED WITH S-P-NITROBENZYLOXYCARBONYLGLUTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qip | ||||||
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Title | HUMAN GLYOXALASE I COMPLEXED WITH S-P-NITROBENZYLOXYCARBONYLGLUTATHIONE | ||||||
Components | PROTEIN (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 / 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 / SYNCHROTRON / OTHER / Resolution: 1.72 Å | ||||||
Authors | Cameron, A.D. / Ridderstrom, M. / Olin, B. / Mannervik, B. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Reaction mechanism of glyoxalase I explored by an X-ray crystallographic analysis of the human enzyme in complex with a transition state analogue. Authors: Cameron, A.D. / Ridderstrom, M. / Olin, B. / Kavarana, M.J. / Creighton, D.J. / Mannervik, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qip.cif.gz | 177.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qip.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 1qip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/1qip ftp://data.pdbj.org/pub/pdb/validation_reports/qi/1qip | HTTPS FTP |
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-Related 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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-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) / Description: HETEROLOGOUSLY EXPRESSED / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 103 / References: UniProt: Q04760, lactoylglutathione lyase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GNB / #4: Chemical | ChemComp-BME / #5: Water | ChemComp-HOH / | Nonpolymer details | COVALENTLY | Sequence details | REFERENCE FOR THE SEQUENCE DATABASE: M.RIDDERSTRO | |
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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: 40 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 Details: PROTEIN WAS CRYSTALLISED BY EQILLABRATION AGAINST PEG 2000 MONOMETHLY ETHER, 50 MM MES PH 5.8, 0.1M NACL THEN SOAKED IN 10MM NBC-GSH | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9123 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: TRIANGULAR MONOCHROMATORN / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9123 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→28 Å / Num. obs: 78648 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 311697 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.72→30 Å / SU B: 2.1 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11 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. DISORDERED SIDE ...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. DISORDERED SIDE CHAINS HAVE BEEN INCLUDED WITH OCCUPANCIES OF 0.
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Displacement parameters | Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→30 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: 3 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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