+Open data
-Basic information
Entry | Database: PDB / ID: 5ie0 | ||||||
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Title | Crystal structure of a plant enzyme | ||||||
Components | Oxalate--CoA ligase | ||||||
Keywords | LIGASE / Arabidopsis / Oxalate degradation | ||||||
Function / homology | Function and homology information seed coat development / oxalate-CoA ligase / oxalate-CoA ligase activity / positive regulation of seed germination / medium-chain fatty acid-CoA ligase activity / oxalate catabolic process / plasmodesma / apoplast / chloroplast stroma / defense response to fungus ...seed coat development / oxalate-CoA ligase / oxalate-CoA ligase activity / positive regulation of seed germination / medium-chain fatty acid-CoA ligase activity / oxalate catabolic process / plasmodesma / apoplast / chloroplast stroma / defense response to fungus / chloroplast / fatty acid metabolic process / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ran, M.R. / Li, M. / Chang, W.R. | ||||||
Citation | Journal: Mol Plant / Year: 2016 Title: Crystal Structures of Arabidopsis thaliana Oxalyl-CoA Synthetase Essential for Oxalate Degradation Authors: Fan, M. / Xiao, Y. / Li, M. / Chang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ie0.cif.gz | 438.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ie0.ent.gz | 357.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ie0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ie0_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 5ie0_full_validation.pdf.gz | 463.4 KB | Display | |
Data in XML | 5ie0_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 5ie0_validation.cif.gz | 75.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/5ie0 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/5ie0 | HTTPS FTP |
-Related structure data
Related structure data | 5ie2C 5ie3C 3a9vS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55613.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AAE3, 4CLL10, AMPBP3, At3g48990, T2J13.170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SMT7, oxalate-CoA ligase #2: Chemical | ChemComp-SRT / #3: 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: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 281 K / Method: evaporation / Details: 0.2M ammonium tartrate dibasic, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 80270 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.2 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A9V Resolution: 2→28.586 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.586 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 140.0872 Å / Origin y: -3.6593 Å / Origin z: 143.8989 Å
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Refinement TLS group | Selection details: all |