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Yorodumi- PDB-4ogg: Crystal Structure of Arabidopsis thaliana DJ-1d with glyoxylate a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ogg | ||||||
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Title | Crystal Structure of Arabidopsis thaliana DJ-1d with glyoxylate as substrate analog | ||||||
Components | Protein DJ-1 homolog D | ||||||
Keywords | LYASE / Glyoxalase | ||||||
Function / homology | Function and homology information glyoxalase III activity / lactoylglutathione lyase / lactoylglutathione lyase activity / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Choi, D. / Kim, J. / Ryu, K.-S. / Park, C. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Stereospecific mechanism of DJ-1 glyoxalases inferred from their hemithioacetal-containing crystal structures. Authors: Choi, D. / Kim, J. / Ha, S. / Kwon, K. / Kim, E.H. / Lee, H.Y. / Ryu, K.S. / Park, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ogg.cif.gz | 245.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ogg.ent.gz | 195.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ogg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ogg_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 4ogg_full_validation.pdf.gz | 462.1 KB | Display | |
Data in XML | 4ogg_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 4ogg_validation.cif.gz | 75.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/4ogg ftp://data.pdbj.org/pub/pdb/validation_reports/og/4ogg | HTTPS FTP |
-Related structure data
Related structure data | 4ofwC 4ogfC 1pdvS C: citing same article (ref.) S: Starting model for refinement |
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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: 41907.539 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DJ1D, At3g02720, F13E7.34 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9M8R4, D-lactate dehydratase #2: 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: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES, 0.1 M sodium chloride, 16% PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 139052 / % possible obs: 97.7 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.088 / Χ2: 1.927 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PDV Resolution: 1.6→50 Å / σ(F): 0
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Displacement parameters | Biso max: 94.49 Å2 / Biso mean: 20.011 Å2 / Biso min: 6.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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