[English] 日本語
Yorodumi- PDB-7ck2: Crystal structure of Arabidopsis CESA3 catalytic domain with UDP-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ck2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Arabidopsis CESA3 catalytic domain with UDP-Glucose | ||||||
Components | Cellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose synthase A catalytic subunit 3 [UDP-forming] | ||||||
Keywords | PLANT PROTEIN / enzyme / synthase | ||||||
Function / homology | Function and homology information plant-type secondary cell wall biogenesis / plant-type primary cell wall biogenesis / cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / plasmodesma / trans-Golgi network / cell wall organization / defense response / : ...plant-type secondary cell wall biogenesis / plant-type primary cell wall biogenesis / cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / plasmodesma / trans-Golgi network / cell wall organization / defense response / : / endosome / Golgi membrane / Golgi apparatus / protein homodimerization activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Qiao, Z. / Gao, Y.G. | ||||||
Funding support | Singapore, 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Structure of Arabidopsis CESA3 catalytic domain with its substrate UDP-glucose provides insight into the mechanism of cellulose synthesis. Authors: Qiao, Z. / Lampugnani, E.R. / Yan, X.F. / Khan, G.A. / Saw, W.G. / Hannah, P. / Qian, F. / Calabria, J. / Miao, Y. / Gruber, G. / Persson, S. / Gao, Y.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ck2.cif.gz | 192.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ck2.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ck2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ck2_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ck2_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7ck2_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 7ck2_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/7ck2 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/7ck2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.994504215634, 0.0323842026337, 0.0995621841138), (-0.00652716024526, -0.968287629882, 0.24975280178), (0.104492876623, 0.247730355906, 0.963177506744)Vector: -1. ...NCS oper: (Code: given Matrix: (-0.994504215634, 0.0323842026337, 0.0995621841138), Vector: |
-Components
#1: Protein | Mass: 45971.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) Gene: CESA3, ATHB, CEV1, ELI1, IXR1, RSW5, At5g05170, K2A11.4 Production host: Escherichia coli (E. coli) References: UniProt: Q941L0, cellulose synthase (UDP-forming) #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.43 % |
---|---|
Crystal grow | Temperature: 291 K / Method: evaporation / Details: PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9735 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9735 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 89995 / % possible obs: 99 % / Redundancy: 14.1 % / Biso Wilson estimate: 48.42 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.98 |
Reflection shell | Resolution: 2.05→2.1 Å / Mean I/σ(I) obs: 0.99 / Num. unique obs: 6579 / CC1/2: 0.98 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.05→43.78 Å / SU ML: 0.2706 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.4689 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→43.78 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.72679252352 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|