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Yorodumi- PDB-6bnx: Crystal structure of V278E-glyoxalase I mutant from Zea mays in s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bnx | ||||||
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Title | Crystal structure of V278E-glyoxalase I mutant from Zea mays in space group P6(3) | ||||||
Components | Lactoylglutathione lyase | ||||||
Keywords | PLANT PROTEIN / PLANT PROTEIN defense | ||||||
Function / homology | Function and homology information lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Alvarez, C.E. / Agostini, R.B. / Gonzalez, J.M. / Drincovich, M.F. / Campos Bermudez, V.A. / Klinke, S. | ||||||
Citation | Journal: Febs J. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bnx.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bnx.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bnx_validation.pdf.gz | 872.9 KB | Display | wwPDB validaton report |
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Full document | 6bnx_full_validation.pdf.gz | 872.9 KB | Display | |
Data in XML | 6bnx_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 6bnx_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/6bnx ftp://data.pdbj.org/pub/pdb/validation_reports/bn/6bnx | HTTPS FTP |
-Related structure data
Related structure data | 6bnnC 6bnzC 5d7zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 / Fragment: residues 26-315 / Mutation: V278E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Plasmid: pET 28b / Details (production host): resistance to kanamycin / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: B6TPH0, lactoylglutathione lyase |
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#2: Chemical | ChemComp-CO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.35 % / Description: needle bunch |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
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: 1.8→41.06 Å / Num. obs: 26692 / % possible obs: 99.9 % / Redundancy: 10.27 % / CC1/2: 1 / Rrim(I) all: 0.067 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 10.32 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4293 / CC1/2: 0.666 / Rrim(I) all: 1.375 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D7Z Resolution: 1.8→41.05 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.8 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126
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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: 38.629 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→41.05 Å
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Refine LS restraints |
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