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- PDB-6bnz: Crystal structure of E144Q-glyoxalase I mutant from Zea mays in s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bnz | ||||||
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Title | Crystal structure of E144Q-glyoxalase I mutant from Zea mays in space group P4(1)2(1)2 | ||||||
![]() | Lactoylglutathione lyase | ||||||
![]() | PLANT PROTEIN / plant protein defense | ||||||
Function / homology | ![]() lactoylglutathione lyase / lactoylglutathione lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alvarez, C.E. / Agostini, R.B. / Gonzalez, J.M. / Drincovich, M.F. / Campos Bermudez, V.A. / Klinke, S. | ||||||
![]() | ![]() 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 | ![]() | 79.1 KB | Display | ![]() |
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PDB format | ![]() | 55.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bnnC ![]() 6bnxC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32958.426 Da / Num. of mol.: 1 / Fragment: residues 26-315 / Mutation: E144Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-CO / | ||
#3: Chemical | ChemComp-GSH / | ||
#4: Chemical | ChemComp-FMT / #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: block |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.7 / Details: sodium formate 4.0 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: Kirkpatrick-Baez pair of bi-morph mirrors |
Radiation | Monochromator: channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→45.68 Å / Num. obs: 53199 / % possible obs: 99.7 % / Redundancy: 12.97 % / CC1/2: 0.999 / Rrim(I) all: 0.068 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.45→1.54 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8395 / CC1/2: 0.731 / Rrim(I) all: 1.946 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5D7Z Resolution: 1.45→45.68 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.726 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.075
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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: 27.318 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→45.68 Å
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Refine LS restraints |
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