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Yorodumi- PDB-6ml3: ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ml3 | ||||||
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Title | ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 2) | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / protein-DNA complex / transcription / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information regulation of immune system process / hematopoietic progenitor cell differentiation / regulation of cytokine production / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.683 Å | ||||||
Authors | Horton, J.R. / Cheng, X. / Ren, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structural basis of specific DNA binding by the transcription factor ZBTB24. Authors: Ren, R. / Hardikar, S. / Horton, J.R. / Lu, Y. / Zeng, Y. / Singh, A.K. / Lin, K. / Coletta, L.D. / Shen, J. / Lin Kong, C.S. / Hashimoto, H. / Zhang, X. / Chen, T. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ml3.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ml3.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ml3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ml3_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 6ml3_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 6ml3_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 6ml3_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/6ml3 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/6ml3 | HTTPS FTP |
-Related structure data
Related structure data | 6ml2SC 6ml4C 6ml5C 6ml6C 6ml7C S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17274.033 Da / Num. of mol.: 1 / Fragment: zinc fingers 4-8 (UNP residues 375-519) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zbtb24, Bif1, Bsg1, Znf450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80X44 |
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-DNA chain , 2 types, 2 molecules EF
#2: DNA chain | Mass: 6168.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) |
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#3: DNA chain | Mass: 6100.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) |
-Non-polymers , 3 types, 82 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-EDO / | #6: 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: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG3350, 0.2 M sodium malonate, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2018 |
Radiation | Monochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→38.361 Å / Num. obs: 48340 / % possible obs: 73.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.039 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 634 / Rpim(I) all: 0.188 / % possible all: 18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6ML2 Resolution: 1.683→38.361 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 43.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.683→38.361 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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