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- PDB-2yy9: Crystal structure of BTB domain from mouse HKR3 -

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Basic information

Entry
Database: PDB / ID: 2yy9
TitleCrystal structure of BTB domain from mouse HKR3
ComponentsZinc finger and BTB domain-containing protein 48
KeywordsTRANSCRIPTION / BTB domain / mouse / HKR3 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / sequence-specific DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / identical protein binding / nucleus / metal ion binding
Similarity search - Function
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 ...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 / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Telomere zinc finger-associated protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsKishishita, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of BTB domain from mouse HKR3
Authors: Kishishita, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 48
B: Zinc finger and BTB domain-containing protein 48


Theoretical massNumber of molelcules
Total (without water)28,4982
Polymers28,4982
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-20.6 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.821, 67.821, 216.487
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-157-

HOH

DetailsThis structure indicate dimer structure in this crystal packing. But, there is no experimental evidence.

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Components

#1: Protein Zinc finger and BTB domain-containing protein 48 / Krueppel-related zinc finger protein 3 / Protein HKR3


Mass: 14248.912 Da / Num. of mol.: 2 / Fragment: BTB domain, UNP residues 8-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hkr3 / Plasmid: PX060116-03 / Production host: cell-free protein synthesis (unknown) / References: UniProt: Q1H9T6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.056M sodium dihydrogen phosphate, 1.344M di-potassium hydrogen phosphate, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9792 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 6, 2006 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 9810 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.3 % / Biso Wilson estimate: 33.2 Å2 / Rsym value: 0.077 / Net I/σ(I): 39.1
Reflection shellResolution: 2.6→2.74 Å / Mean I/σ(I) obs: 10.1 / Rsym value: 0.33

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→45.55 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 83230.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 986 10.3 %RANDOM
Rwork0.226 ---
obs0.226 9533 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8369 Å2 / ksol: 0.391189 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.81 Å24.48 Å20 Å2
2--3.81 Å20 Å2
3----7.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.6→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 64 1731
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 155 10.6 %
Rwork0.277 1312 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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