[English] 日本語
Yorodumi- PDB-2ypf: Structure of the AvrBs3-DNA complex provides new insights into th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ypf | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | TAL effector repeat / TAL effector repeat / DNA / DNA (> 10) / Hax2 Function and homology information | ||||||
Biological species | XANTHOMONAS CAMPESTRIS (bacteria) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Stella, S. / Molina, R. / Yefimenko, I. / Prieto, J. / Silva, G.H. / Bertonati, C. / Juillerat, A. / Duchateau, P. / Montoya, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure of the Avrbs3-DNA Complex Provides New Insights Into the Initial Thymine-Recognition Mechanism Authors: Stella, S. / Molina, R. / Yefimenko, I. / Prieto, J. / Silva, G.H. / Bertonati, C. / Juillerat, A. / Duchateau, P. / Montoya, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ypf.cif.gz | 165 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ypf.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ypf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/2ypf ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2ypf | HTTPS FTP |
---|
-Related structure data
Related structure data | 3v6tS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 78653.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XANTHOMONAS CAMPESTRIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q3ZD73*PLUS |
---|---|
#2: DNA chain | Mass: 6629.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#3: DNA chain | Mass: 6556.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 52 % / Description: NONE |
---|---|
Crystal grow | Details: 0.1M MES PH=6.5, 5-15% PEG3350, 5-15% 2-PROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→32.29 Å / Num. obs: 25764 / % possible obs: 93 % / Observed criterion σ(I): 1.3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.79 |
Reflection shell | Resolution: 2.55→2.62 Å / Redundancy: 2.07 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.31 / % possible all: 95.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3V6T Resolution: 2.55→32.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 25.211 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 0.97 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.161 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→32.29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|