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- PDB-6bnn: Crystal structure of V278E-glyoxalase I mutant from Zea mays in s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bnn | ||||||
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Title | Crystal structure of V278E-glyoxalase I mutant from Zea mays in space group P4(1)2(1)2 | ||||||
![]() | Lactoylglutathione lyase | ||||||
![]() | PLANT PROTEIN | ||||||
Function / homology | ![]() lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alvarez, C.E. / Agostini, R.B. / Gonzalez, J.M. / Drincovich, M.F. / Campos Bermudez, V.A. / Klinke, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Deciphering the number and location of active sites in the monomeric glyoxalase I of Zea mays. Authors: Gonzalez, J.M. / Agostini, R.B. / Alvarez, C.E. / Klinke, S. / Andreo, C.S. / Campos-Bermudez, V.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.7 KB | Display | ![]() |
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PDB format | ![]() | 55.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bnxC ![]() 6bnzC ![]() 5d7zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 32989.395 Da / Num. of mol.: 1 / Mutation: V278E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-GSH / | ||
#3: Chemical | ChemComp-CO / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % / Description: oval |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.7 / Details: sodium formate 4.2 M pH 9.7 0.5% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016 Details: convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors |
Radiation | Monochromator: cryogenically cooled channel cut crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→45.7 Å / Num. obs: 43782 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rrim(I) all: 0.065 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.55→1.64 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6880 / CC1/2: 0.684 / Rrim(I) all: 1.653 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5D7Z Resolution: 1.55→45.7 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.015 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.089
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.367 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→45.7 Å
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Refine LS restraints |
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