+Open data
-Basic information
Entry | Database: PDB / ID: 4osm | ||||||
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Title | Crystal structure of the S505H mutant of TAL effector dHax3 | ||||||
Components |
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Keywords | DNA binding protein/DNA / DNA binding protein / DNA / DNA binding protein-DNA complex | ||||||
Function / homology | : / TAL effector repeat / TAL effector repeat / DNA / DNA (> 10) / Hax3 Function and homology information | ||||||
Biological species | Xanthomonas campestris pv. armoraciae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.454 Å | ||||||
Authors | Deng, D. / Wu, J.P. / Yan, C.Y. / Pan, X.J. / Yan, N. | ||||||
Citation | Journal: Protein Cell / Year: 2014 Title: Revisiting the TALE repeat Authors: Deng, D. / Yan, C.Y. / Wu, J.P. / Pan, X.J. / Yan, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4osm.cif.gz | 427.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4osm.ent.gz | 349.5 KB | Display | PDB format |
PDBx/mmJSON format | 4osm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4osm_validation.pdf.gz | 471.5 KB | Display | wwPDB validaton report |
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Full document | 4osm_full_validation.pdf.gz | 497.5 KB | Display | |
Data in XML | 4osm_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 4osm_validation.cif.gz | 58 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/4osm ftp://data.pdbj.org/pub/pdb/validation_reports/os/4osm | HTTPS FTP |
-Related structure data
Related structure data | 4oshC 4osiC 4osjC 4oskC 4oslC 4osqC 4osrC 4ossC 4ostC 4osvC 4oswC 4oszC 4ot0C 4ot3C 4otoC 3v6tS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51805.574 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720 Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505H,S539G,N572H,S573D,H606N,D607G,N640H,I641D 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 #2: DNA chain | Mass: 5070.281 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 5342.513 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Water | ChemComp-HOH / | |
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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: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10%-15% PEG 3350, 12% ethanol, 0.1M MES, pH 6.0, 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: 0.9785 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→41.77 Å / Num. all: 44029 / Num. obs: 44006 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V6T Resolution: 2.454→41.769 Å / FOM work R set: 0.7944 / SU ML: 0.44 / σ(F): 1.34 / Phase error: 27.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.718 Å2 / ksol: 0.307 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.47 Å2 / Biso mean: 33.38 Å2 / Biso min: 4.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.454→41.769 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: 16
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Refinement TLS params. | Method: refined / Origin x: -34.3391 Å / Origin y: 14.7695 Å / Origin z: -18.5632 Å
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Refinement TLS group | Selection details: ALL |