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Yorodumi- PDB-4f6m: Crystal structure of Kaiso zinc finger DNA binding domain in comp... -
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-Basic information
Entry | Database: PDB / ID: 4f6m | ||||||
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Title | Crystal structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding site DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / zinc finger / protein-DNA complex / double helix / DNA binding / DNA / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Buck-Koehntop, B.A. / Stanfield, R.L. / Ekiert, D.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso. Authors: Buck-Koehntop, B.A. / Stanfield, R.L. / Ekiert, D.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f6m.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f6m.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 4f6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/4f6m ftp://data.pdbj.org/pub/pdb/validation_reports/f6/4f6m | HTTPS FTP |
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-Related 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: 16086.575 Da / Num. of mol.: 1 / Fragment: zinc finger DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB33, KAISO, ZNF348 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[DNAY] / References: UniProt: Q86T24 | ||
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#2: DNA chain | Mass: 5780.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs in humans / Source: (synth.) Homo sapiens (human) | ||
#3: DNA chain | Mass: 5869.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs in humans / Source: (synth.) Homo sapiens (human) | ||
#4: Chemical | #5: 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: 4.19 Å3/Da / Density % sol: 70.67 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2M sodium nitrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.2819 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2819 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 18774 / Num. obs: 18774 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.67 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 4.64 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.8 / Num. unique all: 927 / Rsym value: 0.515 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→34.69 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→34.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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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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