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- PDB-8qeu: Crystal structure of ornithine transcarbamylase from Arabidopsis ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qeu | ||||||
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Title | Crystal structure of ornithine transcarbamylase from Arabidopsis thaliana (AtOTC) in complex with ornithine | ||||||
![]() | Ornithine transcarbamylase, chloroplastic![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nielipinski, M. / Pietrzyk-Brzezinska, A. / Sekula, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae . Authors: Nielipinski, M. / Pietrzyk-Brzezinska, A.J. / Wlodawer, A. / Sekula, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.9 KB | Display | ![]() |
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PDB format | ![]() | 354.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8qevC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 3 molecules ABC
#1: Protein | ![]() Mass: 35750.836 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: O50039, ![]() |
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-Non-polymers , 6 types, 1307 molecules ![](data/chem/img/ORN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ORN / ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-EDO / ![]() #5: Chemical | ChemComp-SO4 / ![]() #6: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.7 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 3350 16%, Lithium sulfate 0.3M, HEPES 0.1M pH 6.0, 20mM ornithine, cryoprotection was obtained by 25% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2023 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→50 Å / Num. obs: 208445 / % possible obs: 99.6 % / Redundancy: 7.33 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.88 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 7.14 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 33258 / CC1/2: 0.731 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.788 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→49.02 Å
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Refine LS restraints |
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