+Open data
-Basic information
Entry | Database: PDB / ID: 6ryd | ||||||
---|---|---|---|---|---|---|---|
Title | WUS-HD bound to TGAA DNA | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / Homeodomain Transcription factor | ||||||
Function / homology | Function and homology information stomium development / anther development / axillary shoot meristem initiation / stem cell population maintenance / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.575 Å | ||||||
Authors | Sloan, J.J. / Wild, K. / Sinning, I. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL. Authors: Sloan, J. / Hakenjos, J.P. / Gebert, M. / Ermakova, O. / Gumiero, A. / Stier, G. / Wild, K. / Sinning, I. / Lohmann, J.U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ryd.cif.gz | 199.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ryd.ent.gz | 154.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ryd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ryd_validation.pdf.gz | 471.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ryd_full_validation.pdf.gz | 473.6 KB | Display | |
Data in XML | 6ryd_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 6ryd_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/6ryd ftp://data.pdbj.org/pub/pdb/validation_reports/ry/6ryd | HTTPS FTP |
-Related structure data
Related structure data | 6ry3SC 6ryiC 6rylC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8949.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WUS, PGA6, At2g17950, T27K22.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SB92 #2: DNA chain | Mass: 4986.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) #3: DNA chain | Mass: 4808.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.9 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate (pH 4.6), 8% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.575→43.62 Å / Num. obs: 59197 / % possible obs: 98.82 % / Redundancy: 3.4 % / Rpim(I) all: 0.02557 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 1.575→1.631 Å / Num. unique obs: 5914 / CC1/2: 0.778 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RY3 Resolution: 1.575→34.38 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / Phase error: 24.95
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.83 Å2 / Biso mean: 38.701 Å2 / Biso min: 14.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.575→34.38 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
|