+Open data
-Basic information
Entry | Database: PDB / ID: 3m4t | ||||||
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Title | Crystal structure of the BTB domain from Kaiso/ZBTB33, form I | ||||||
Components | Transcriptional regulator Kaiso | ||||||
Keywords | TRANSCRIPTION / Kaiso / ZBTB33 / Transcriptional regulator Kaiso / Zinc finger and BTB domain-containing protein 33 / ZNF348 / Protein-protein interaction domain / oligomeriation / BTB domain / POZ domain / BTB/POZ domain / ZINC-FINGER PROTEIN / Activator / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Repressor / Transcription regulation / Wnt signaling pathway / Zinc-finger | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Stogios, P.J. / Chen, L. / Prive, G.G. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of the BTB domain from Kaiso/ZBTB33, form I Authors: Stogios, P.J. / Nielsen, T.K. / Chen, L. / Prive, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m4t.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m4t.ent.gz | 25.1 KB | Display | PDB format |
PDBx/mmJSON format | 3m4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/3m4t ftp://data.pdbj.org/pub/pdb/validation_reports/m4/3m4t | HTTPS FTP |
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-Related structure data
Related structure data | 1buoS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13852.873 Da / Num. of mol.: 1 / Fragment: BTB domain from Kaiso/ZBTB33, UNP residues 1-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KAISO, ZBTB33, ZNF348 / Plasmid: pET-32(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q86T24 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.75 Å3/Da / Density % sol: 55.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: 0.25 M sodium sulfate, 0.1 M sodium acetate pH 4.3, 13% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 6, 2004 / Details: mirrors |
Radiation | Monochromator: Si (111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→29.3 Å / Num. obs: 10103 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 20.95 % / Rsym value: 0.065 / Net I/σ(I): 51.82 |
Reflection shell | Resolution: 2.05→2.12 Å / Mean I/σ(I) obs: 8.43 / Num. unique all: 980 / Rsym value: 0.347 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Single chain poly-alanine model of PDB code 1BUO, except where residues were identical between Kaiso and 1BUO, and all loops and turns were deleted Resolution: 2.05→29.3 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.425 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.704 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→29.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.101 Å / Total num. of bins used: 20
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