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Yorodumi- PDB-9ggi: Crystal structure of argininosuccinate lyase from Arabidopsis tha... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9ggi | ||||||
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| Title | Crystal structure of argininosuccinate lyase from Arabidopsis thaliana (AtASL) | ||||||
Components | Argininosuccinate lyase, chloroplastic | ||||||
Keywords | LYASE / arginine / urea cycle / complex / argininosuccinate | ||||||
| Function / homology | Function and homology informationargininosuccinate lyase / argininosuccinate lyase activity / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / chloroplast stroma / chloroplast Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Nielipinski, M. / Pietrzyk-Brzezinska, A.J. / Krzeszewska, D. / Sekula, B. | ||||||
| Funding support | Poland, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2024Title: Arabidopsis thaliana argininosuccinate lyase structure uncovers the role of serine as the catalytic base. Authors: Nielipinski, M. / Nielipinska, D. / Pietrzyk-Brzezinska, A.J. / Sekula, B. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9ggi.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9ggi.ent.gz | 1.2 MB | Display | PDB format |
| PDBx/mmJSON format | 9ggi.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9ggi_validation.pdf.gz | 535.5 KB | Display | wwPDB validaton report |
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| Full document | 9ggi_full_validation.pdf.gz | 570.6 KB | Display | |
| Data in XML | 9ggi_validation.xml.gz | 199.1 KB | Display | |
| Data in CIF | 9ggi_validation.cif.gz | 280.1 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/9ggi ftp://data.pdbj.org/pub/pdb/validation_reports/gg/9ggi | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9ggjC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
| #1: Protein | Mass: 51979.062 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 5 types, 4558 molecules 








| #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.07 % |
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| Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M BIS-TRIS pH 5.5, 2.0M Ammonium sulfate |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976 Å |
| Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2023 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
| Reflection | Resolution: 1.55→48.48 Å / Num. obs: 720570 / % possible obs: 94.1 % / Redundancy: 2.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.061 / Net I/σ(I): 13 |
| Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 73727 / CC1/2: 0.55 / Rrim(I) all: 0.775 / % possible all: 96.4 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→48.45 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.591 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.059 / 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: 22.517 Å2
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| Refinement step | Cycle: 1 / Resolution: 1.55→48.45 Å
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| Refine LS restraints |
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X-RAY DIFFRACTION
Poland, 1items
Citation
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