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Open data
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Basic information
Entry | Database: PDB / ID: 6ypo | |||||||||
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Title | Arabidopsis aspartate transcarbamoylase bound to 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 | ![]() | 453.1 KB | Display | ![]() |
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PDB format | ![]() | 322.9 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 | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ys6C ![]() 6yspC ![]() 6yvbC ![]() 6yw9C ![]() 6ywjC ![]() 6yy1C ![]() 5g1nS 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37188.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #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: 54.62 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion Details: Protein at 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2 % glycerol and 0.2 mM tris(2-carboxyethyl) phosphine (TCEP). Crystallization reservoir: 22 % PEG 3350, 0.1 M sodium sulfate, 0.1 M bis-tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→90.54 Å / Num. obs: 91035 / % possible obs: 99.38 % / Redundancy: 10.3 % / Biso Wilson estimate: 28.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1046 / Net I/σ(I): 12.74 |
Reflection shell | Resolution: 1.67→1.73 Å / Redundancy: 10 % / Rmerge(I) obs: 1.396 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 9119 / CC1/2: 0.601 / % possible all: 99.99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5G1N Resolution: 1.67→90.54 Å / Cross valid method: FREE R-VALUE / σ(F): 21.86 / Phase error: 25.6742 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→90.54 Å
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Refine LS restraints |
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LS refinement shell |
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