+Open data
-Basic information
Entry | Database: PDB / ID: 6ypo | |||||||||
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Title | Arabidopsis aspartate transcarbamoylase bound to 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: 1.67 Å | |||||||||
Authors | Ramon Maiques, S. / Del Cano Ochoa, F. / Bellin, L. / Mohlmann, T. | |||||||||
Funding support | Spain, 2items
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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 | 6ypo.cif.gz | 453.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ypo.ent.gz | 322.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ypo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypo ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypo | HTTPS FTP |
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-Related structure data
Related structure data | 6ys6C 6yspC 6yvbC 6yw9C 6ywjC 6yy1C 5g1nS 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 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.) 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 | ChemComp-GOL / #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: 54.62 % |
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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: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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