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- PDB-3m52: Crystal structure of the BTB domain from the Miz-1/ZBTB17 transcr... -
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Basic information
Entry | Database: PDB / ID: 3m52 | ||||||
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Title | Crystal structure of the BTB domain from the Miz-1/ZBTB17 transcription regulator | ||||||
![]() | Zinc finger and BTB domain-containing protein 17 | ||||||
![]() | TRANSCRIPTION / BTB domain / POZ domain / BTB/POZ domain / Miz-1 / Zinc finger protein 151 / Myc-interacting zinc finger protein / Miz-1 protein / ZFP151 / ZFP-151 / ZNF151 / MIZ1 / Zinc finger and BTB domain-containing protein 17 / Zinc finger protein 60 / Protein-protein interaction domain / transcription regulator / transcription activator / ZINC-FINGER PROTEIN / alpha/beta protein / Developmental protein / DNA-binding / Metal-binding / Nucleus / Transcription regulation / Zinc-finger / DNA BINDING PROTEIN | ||||||
Function / homology | ![]() ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding ...ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stogios, P.J. / Cuesta-Seijo, J.A. / Chen, L. / Prive, G.G. | ||||||
![]() | ![]() Title: Insights into Strand Exchange in BTB Domain Dimers from the Crystal Structures of FAZF and Miz1. Authors: Stogios, P.J. / Cuesta-Seijo, J.A. / Chen, L. / Pomroy, N.C. / Prive, G.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.5 KB | Display | ![]() |
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PDB format | ![]() | 42.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3m5bC ![]() 1r29S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12934.875 Da / Num. of mol.: 2 / Fragment: BTB domain from Miz-1/ZBTB17 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 75 mM zinc acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2006 / Details: mirrors |
Radiation | Monochromator: Double-crystal monochromator Si-111 Double-crystal monochromator Si-220 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→90 Å / Num. obs: 8404 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.67 % / Rsym value: 0.0952 / Net I/σ(I): 10.87 |
Reflection shell | Resolution: 2.59→2.7 Å / Redundancy: 0.96 % / Mean I/σ(I) obs: 3.55 / Num. unique all: 92 / Rsym value: 0.4483 / % possible all: 48.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Single chain poly-alanine model of PDB code 1R29 residues 7-128, except where residues were identical between Miz1 and 1R29 Resolution: 2.59→41.2 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.885 / SU B: 12.233 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 1.026 / ESU R Free: 0.338 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.383 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→41.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.657 Å / Total num. of bins used: 20
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