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- PDB-3m8v: Crystal structure of the BTB domain from Kaiso/ZBTB33, form II -

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Basic information

Entry
Database: PDB / ID: 3m8v
TitleCrystal structure of the BTB domain from Kaiso/ZBTB33, form II
ComponentsTranscriptional regulator Kaiso
KeywordsTRANSCRIPTION / 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 / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
: / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / 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. / 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
Transcriptional regulator Kaiso
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNielsen, T.K. / Stogios, P.J. / Prive, G.G.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the BTB domain from Kaiso/ZBTB33, form II
Authors: Stogios, P.J. / Nielsen, T.K. / Chen, L. / Prive, G.G.
History
DepositionMar 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Transcriptional regulator Kaiso


Theoretical massNumber of molelcules
Total (without water)13,8531
Polymers13,8531
Non-polymers00
Water36020
1
A: Transcriptional regulator Kaiso

A: Transcriptional regulator Kaiso


Theoretical massNumber of molelcules
Total (without water)27,7062
Polymers27,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3410 Å2
ΔGint-20 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.797, 114.797, 62.228
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Transcriptional regulator Kaiso / Zinc finger and BTB domain-containing protein 33


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 4.27 Å3/Da / Density % sol: 71.21 %
Crystal growTemperature: 295 K / pH: 4.3
Details: 0.9 M ammonium citrate, 0.1 M sodium acetate pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 12, 2008 / Details: OSMIC MULTI-LAYER OPTICS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 7037 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rsym value: 0.069 / Net I/σ(I): 35.01
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 5.86 / Rsym value: 0.424 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.6.3_473refinement
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M4T

3m4t


Resolution: 2.7→28.699 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU ML: 0.22 / σ(F): 1.33 / Phase error: 24.84 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2442 331 4.74 %
Rwork0.2005 --
obs0.2025 6986 99.28 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.416 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3896 Å20 Å20 Å2
2---0.3896 Å2-0 Å2
3---0.7792 Å2
Refinement stepCycle: LAST / Resolution: 2.7→28.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 0 20 925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008918
X-RAY DIFFRACTIONf_angle_d1.2071235
X-RAY DIFFRACTIONf_dihedral_angle_d15.881336
X-RAY DIFFRACTIONf_chiral_restr0.078145
X-RAY DIFFRACTIONf_plane_restr0.003155
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8652-0.2674-0.70720.48860.13220.99290.46250.50470.24050.09320.00920.2423-0.3854-0.4845-0.00640.27390.06330.03890.3523-0.13540.2161-27.4846-35.81611.1572
22.6498-0.7257-1.06141.83570.59830.83680.05920.17390.1225-0.05370.188-0.32820.0498-0.04470.00340.19130.00430.15920.2850.00150.2491-10.8316-38.8186-12.0456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1resid 4:32
2X-RAY DIFFRACTION2resid 33:117

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