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- PDB-6ywj: Arabidopsis aspartate transcarbamoylase mutant F161A complex with UMP -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ywj | |||||||||||||||
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Title | Arabidopsis aspartate transcarbamoylase mutant F161A complex with UMP | |||||||||||||||
![]() | PYRB | |||||||||||||||
![]() | PLANT PROTEIN / Transferase / chloroplast / pyrimidine de novo biosynthesis | |||||||||||||||
Function / homology | ![]() aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / cellular response to phosphate starvation / amino acid metabolic process / amino acid binding / chloroplast stroma / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / chloroplast / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Ramon Maiques, S. / Del Cano Ochoa, F. / Bellin, L. / Mohlmann, T. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141 KB | Display | ![]() |
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PDB format | ![]() | 105.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ypoSC ![]() 6ys6C ![]() 6yspC ![]() 6yvbC ![]() 6yw9C ![]() 6yy1C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 37112.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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