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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
TitleCrystal structure of the BTB domain from the Miz-1/ZBTB17 transcription regulator
ComponentsZinc finger and BTB domain-containing protein 17
KeywordsTRANSCRIPTION / 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
Function and homology information


ectoderm development / XBP1(S) activates chaperone genes / gastrulation with mouth forming second / regulation of immune system process / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific ...ectoderm development / XBP1(S) activates chaperone genes / gastrulation with mouth forming second / regulation of immune system process / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / 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 / zinc ion binding / nucleoplasm
Similarity search - Function
C2H2-type zinc finger / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. ...C2H2-type zinc finger / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Zinc finger and BTB domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsStogios, P.J. / Cuesta-Seijo, J.A. / Chen, L. / Prive, G.G.
CitationJournal: J.Mol.Biol. / Year: 2010
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
DepositionMar 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 17
B: Zinc finger and BTB domain-containing protein 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38010
Polymers25,8702
Non-polymers5118
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-193 kcal/mol
Surface area12010 Å2
MethodPISA
2
A: Zinc finger and BTB domain-containing protein 17
hetero molecules

B: Zinc finger and BTB domain-containing protein 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38010
Polymers25,8702
Non-polymers5118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1380 Å2
ΔGint-158 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.023, 80.935, 95.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Zinc finger and BTB domain-containing protein 17 / Zinc finger protein 60 / Zinc finger protein 151 / Myc-interacting zinc finger protein 1 / Miz-1


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.) Homo sapiens (human) / Gene: MIZ1, ZBTB17, ZNF151, ZNF60 / Plasmid: pET-32(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q13105
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 75 mM zinc acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2006 / Details: mirrors
RadiationMonochromator: Double-crystal monochromator Si-111 Double-crystal monochromator Si-220
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
ADSCQuantumdata collection
EPMRphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Single chain poly-alanine model of PDB code 1R29 residues 7-128, except where residues were identical between Miz1 and 1R29

1r29

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 383 4.6 %RANDOM
Rwork0.22493 ---
obs0.22688 7990 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.383 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.59→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 14 44 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9512462
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8725232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80725.87580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46615309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.74152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021353
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21236
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.080.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4311.51197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.821853
X-RAY DIFFRACTIONr_scbond_it1.2583695
X-RAY DIFFRACTIONr_scangle_it1.6444.5609
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 33 -
Rwork0.271 531 -
obs--93.38 %

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