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- PDB-4f6m: Crystal structure of Kaiso zinc finger DNA binding domain in comp... -

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Basic information

Entry
Database: PDB / ID: 4f6m
TitleCrystal structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding site DNA
Components
  • DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
  • Transcriptional regulator Kaiso
KeywordsDNA BINDING PROTEIN/DNA / zinc finger / protein-DNA complex / double helix / DNA binding / DNA / DNA BINDING PROTEIN-DNA complex
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
Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily ...Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Double Stranded RNA Binding 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
DNA / DNA (> 10) / Transcriptional regulator Kaiso
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBuck-Koehntop, B.A. / Stanfield, R.L. / Ekiert, D.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso.
Authors: Buck-Koehntop, B.A. / Stanfield, R.L. / Ekiert, D.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Transcriptional regulator Kaiso
D: DNA (5'-D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
E: DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9336
Polymers27,7373
Non-polymers1963
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-32 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.760, 185.180, 112.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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


Mass: 16086.575 Da / Num. of mol.: 1 / Fragment: zinc finger DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB33, KAISO, ZNF348 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[DNAY] / References: UniProt: Q86T24
#2: DNA chain DNA (5'-D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')


Mass: 5780.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs in humans / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3')


Mass: 5869.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs in humans / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 4.19 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium nitrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.2819 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2819 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 18774 / Num. obs: 18774 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.67 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 11.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.64 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.8 / Num. unique all: 927 / Rsym value: 0.515 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→34.69 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23986 950 5.1 %RANDOM
Rwork0.22212 ---
all0.22306 18773 --
obs0.22306 18773 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 773 3 83 1835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211939
X-RAY DIFFRACTIONr_angle_refined_deg1.8382.4472715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8095117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.15920.76952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.0515181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8231512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021175
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 69 -
Rwork0.382 1292 -
obs-1361 99.56 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.3511-0.39850.37288.7515-0.42571.2941-0.06170.05780.1543-0.40870.0750.448-0.3758-0.0038-0.01330.1444-0.0175-0.01990.1139-0.01420.149215.035765.079829.6909
24.7128-0.30040.88037.34980.570910.6076-0.09910.15890.0281-0.38460.26070.3649-0.1061-0.2875-0.16160.0338-0.0397-0.03040.1016-0.00270.142614.776667.485826.6934
37.2193-0.89081.2538.6824-0.52886.8806-0.22090.25380.3591-0.37070.2040.5622-0.8283-0.06260.01690.1273-0.014-0.04240.03080.03140.105814.966368.525526.3774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A482 - 597
2X-RAY DIFFRACTION2D1 - 19
3X-RAY DIFFRACTION3E20 - 38

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