+Open data
-Basic information
Entry | Database: PDB / ID: 6yy1 | |||||||||||||||
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Title | Arabidopsis aspartate transcarbamoylase in apo state | |||||||||||||||
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 / cytosol Similarity search - Function | |||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 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 | 6yy1.cif.gz | 825.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yy1.ent.gz | 556.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yy1_validation.pdf.gz | 479.1 KB | Display | wwPDB validaton report |
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Full document | 6yy1_full_validation.pdf.gz | 493.4 KB | Display | |
Data in XML | 6yy1_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 6yy1_validation.cif.gz | 83.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/6yy1 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/6yy1 | HTTPS FTP |
-Related structure data
Related structure data | 6ypoSC 6ys6C 6yspC 6yvbC 6yw9C 6ywjC 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: 37188.488 Da / Num. of mol.: 6 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: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.82 Å3/Da / Density % sol: 56.35 % |
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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). Crystallization solution was 18-22% PEG 3350 and 150-200 mM potassium ...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). Crystallization solution was 18-22% PEG 3350 and 150-200 mM potassium acetate. Crystals were cryo-protected by soaking in a solution containing the mother liquor supplemented with 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→92.85 Å / Num. obs: 45073 / % possible obs: 99.29 % / Redundancy: 5.2 % / Biso Wilson estimate: 66.92 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.16 |
Reflection shell | Resolution: 3.06→3.18 Å / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 4435 / CC1/2: 0.686 / % possible all: 99.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YPO Resolution: 3.06→92.85 Å / SU ML: 0.3908 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1086
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.06→92.85 Å
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Refine LS restraints |
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LS refinement shell |
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