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Yorodumi- PDB-6ywj: Arabidopsis aspartate transcarbamoylase mutant F161A complex with UMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ywj | |||||||||||||||
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Title | Arabidopsis aspartate transcarbamoylase mutant F161A complex with UMP | |||||||||||||||
Components | PYRB | |||||||||||||||
Keywords | PLANT PROTEIN / Transferase / chloroplast / pyrimidine de novo biosynthesis | |||||||||||||||
Function / homology | Function and homology information aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / cellular response to phosphate starvation / amino acid metabolic process / chloroplast stroma / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / chloroplast Similarity search - Function | |||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||||||||
Authors | Ramon Maiques, S. / Del Cano Ochoa, F. / Bellin, L. / Mohlmann, T. | |||||||||||||||
Funding support | Spain, Germany, 4items
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Citation | Journal: Nat Commun / Year: 2021 Title: Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase. Authors: Bellin, L. / Del Cano-Ochoa, F. / Velazquez-Campoy, A. / Mohlmann, T. / Ramon-Maiques, S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ywj.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ywj.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ywj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6ywj ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6ywj | HTTPS FTP |
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-Related structure data
Related structure data | 6ypoSC 6ys6C 6yspC 6yvbC 6yw9C 6yy1C S: Starting model for refinement C: citing same article (ref.) |
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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: 37112.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At3g21670 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A178VJE3, UniProt: P49077*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: Protein at 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2% glycerol, 0.2 mM tris(2-carboxyethyl) phosphine (TCEP) and with 5 mM UMP. Crystallization solution: 18-22 % PEG3350, 0.1 M ...Details: Protein at 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2% glycerol, 0.2 mM tris(2-carboxyethyl) phosphine (TCEP) and with 5 mM UMP. Crystallization solution: 18-22 % PEG3350, 0.1 M Na2SO4 and 0.1 M bis-tris pH 6.5 Crystals were cryo-protected by soaking in a solution containing the mother liquor supplemented with 20% glycerol and the 5 mM UMP. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2019 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→48.304 Å / Num. obs: 30917 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.992 / Rmerge(I) obs: 0.194 / Net I/σ(I): 8.5 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 2 / Num. unique obs: 3526 / CC1/2: 0.629 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YPO Resolution: 2.4→48.304 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.608 / SU ML: 0.091 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.04 Details: Hydrogens have been added in their 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→48.304 Å
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Refine LS restraints |
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LS refinement shell |
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