+Open data
-Basic information
Entry | Database: PDB / ID: 8u8l | ||||||
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Title | X-ray crystal structure of TEBP-2 MCD3 with ds DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Telomeres / C. elegans / shelterin / DNA-binding protein / TEBP-2 / DTN-2 / MYB / homeodomain / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | DNA binding / : / DNA / DNA (> 10) / Double-strand telomeric DNA-binding proteins 2 Function and homology information | ||||||
Biological species | Caenorhabditis elegans (invertebrata) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nandakumar, J. / Padmanaban, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Caenorhabditis elegans telomere-binding proteins TEBP-1 and TEBP-2 adapt the Myb module to dimerize and bind telomeric DNA. Authors: Padmanaban, S. / Lambacher, N.J. / Tesmer, V.M. / Zhang, J. / Shibuya, H. / Nandakumar, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u8l.cif.gz | 112.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u8l.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 8u8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u8l_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 8u8l_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 8u8l_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 8u8l_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/8u8l ftp://data.pdbj.org/pub/pdb/validation_reports/u8/8u8l | HTTPS FTP |
-Related structure data
Related structure data | 8u8mC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14716.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tebp-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q22429 #2: DNA chain | | Mass: 5866.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 5757.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-CS / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.13 Å3/Da / Density % sol: 60.66 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: TEBP-2 MCD3 DNA + 100 mM MES, pH 6.5, 21% PEG8000, 50 mM sodium chloride, 100 mM cesium chloride, sitting drop, 16 degrees C, cryoprotectant: 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12723 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→83.23 Å / Num. obs: 50213 / % possible obs: 99.6 % / Redundancy: 10.7 % / Biso Wilson estimate: 38.16 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 3 / Num. unique obs: 2738 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→52.98 Å / SU ML: 0.2697 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3295 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→52.98 Å
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Refine LS restraints |
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LS refinement shell |
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