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Yorodumi- PDB-4gg4: Crystal structure of the TAL effector dHax3 bound to specific DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gg4 | ||||||
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Title | Crystal structure of the TAL effector dHax3 bound to specific DNA-RNA hybrid | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA/RNA / tandem repeat / TAL effector / sequence specific DNA binding protein / DNA duplex / DNA-RNA hybrid / DNA BINDING PROTEIN-DNA-RNA complex | ||||||
Function / homology | : / TAL effector repeat / TAL effector repeat / DNA / DNA (> 10) / RNA / RNA (> 10) / Hax3 Function and homology information | ||||||
Biological species | Xanthomonas campestris pv. armoraciae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å | ||||||
Authors | Yin, P. / Deng, D. / Yan, C.Y. / Pan, X.J. / Yan, N. / Shi, Y.G. | ||||||
Citation | Journal: Cell Rep / Year: 2012 Title: Specific DNA-RNA hybrid recognition by TAL effectors Authors: Yin, P. / Deng, D. / Yan, C. / Pan, X.J. / Xi, J.J. / Yan, N. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gg4.cif.gz | 226.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gg4.ent.gz | 176.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gg4_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 4gg4_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 4gg4_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 4gg4_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/4gg4 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/4gg4 | HTTPS FTP |
-Related structure data
Related structure data | 3v6tS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51780.586 Da / Num. of mol.: 1 / Fragment: TAL effector, UNP residues 231-720 / Mutation: multiple mutations Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. armoraciae (bacteria) Gene: hax3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZD72 |
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#2: DNA chain | Mass: 5070.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This DNA oligo was ordered from Takara |
#3: RNA chain | Mass: 5600.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This RNA oligo was ordered from Takara |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 11% PEG 3350 (w/v), 12% ethanol, 0.1M MES pH6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.00915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2011 |
Radiation | Monochromator: Si 111 CHANNE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00915 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 26222 / Num. obs: 25803 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 47.42 Å2 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V6T Resolution: 2.501→31.725 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8139 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 25.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.337 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.82 Å2 / Biso mean: 50.2915 Å2 / Biso min: 22.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.501→31.725 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 49.8698 Å / Origin y: -16.5325 Å / Origin z: -10.3553 Å
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Refinement TLS group | Selection details: all |