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Yorodumi- PDB-8qev: Crystal structure of ornithine transcarbamylase from Arabidopsis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qev | ||||||
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Title | Crystal structure of ornithine transcarbamylase from Arabidopsis thaliana (AtOTC) in complex with carbamoyl phosphate | ||||||
Components | Ornithine transcarbamylase, chloroplastic | ||||||
Keywords | TRANSFERASE / transcarbamylase / carbamoyl transferase / urea cycle / arginine biosynthesis | ||||||
Function / homology | Function and homology information ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process / chloroplast stroma / amino acid binding / chloroplast Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Nielipinski, M. / Pietrzyk-Brzezinska, A. / Sekula, B. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Front Plant Sci / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qev.cif.gz | 384 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qev.ent.gz | 313.4 KB | Display | PDB format |
PDBx/mmJSON format | 8qev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/8qev ftp://data.pdbj.org/pub/pdb/validation_reports/qe/8qev | HTTPS FTP |
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-Related structure data
Related structure data | 8qeuC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Arabidopsis thaliana (thale cress) / Gene: OTC, At1g75330, F1B16.13 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O50039, ornithine carbamoyltransferase |
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-Non-polymers , 7 types, 1223 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.29 Å3/Da / Density % sol: 62.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 3350 26%, Lithium sulfate 0.3M, HEPES 0.1M pH 6.0, 20mM carbamoyl phosphate, cryoprotection was obtained by 25% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
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: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 194853 / % possible obs: 99.2 % / Redundancy: 5.51 % / CC1/2: 0.982 / Rmerge(I) obs: 0.172 / Net I/σ(I): 5.25 |
Reflection shell | Resolution: 1.55→1.64 Å / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 30724 / CC1/2: 0.563 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→44.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.045 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 20.606 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→44.67 Å
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