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- PDB-6ml3: ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 2) -

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Basic information

Entry
Database: PDB / ID: 6ml3
TitleZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 2)
Components
  • DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*AP*GP*CP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*GP*CP*TP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')
  • Zinc finger and BTB domain-containing protein 24
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / transcription / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


hematopoietic progenitor cell differentiation / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleus
Similarity search - Function
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
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger and BTB domain-containing protein 24
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.683 Å
AuthorsHorton, J.R. / Cheng, X. / Ren, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis of specific DNA binding by the transcription factor ZBTB24.
Authors: Ren, R. / Hardikar, S. / Horton, J.R. / Lu, Y. / Zeng, Y. / Singh, A.K. / Lin, K. / Coletta, L.D. / Shen, J. / Lin Kong, C.S. / Hashimoto, H. / Zhang, X. / Chen, T. / Cheng, X.
History
DepositionSep 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 24
E: DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*AP*GP*CP*TP*AP*A)-3')
F: DNA (5'-D(*TP*TP*TP*AP*GP*CP*TP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9329
Polymers29,5433
Non-polymers3896
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-43 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.297, 68.757, 50.010
Angle α, β, γ (deg.)90.00, 93.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Zinc finger and BTB domain-containing protein 24 / Bone morphogenetic protein-induced factor 1 / Brain-specific protein 1 / Zinc finger protein 450


Mass: 17274.033 Da / Num. of mol.: 1 / Fragment: zinc fingers 4-8 (UNP residues 375-519)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zbtb24, Bif1, Bsg1, Znf450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80X44

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*AP*GP*CP*TP*AP*A)-3')


Mass: 6168.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(*TP*TP*TP*AP*GP*CP*TP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')


Mass: 6100.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 3 types, 82 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG3350, 0.2 M sodium malonate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2018
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→38.361 Å / Num. obs: 48340 / % possible obs: 73.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.039 / Net I/σ(I): 14.6
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 634 / Rpim(I) all: 0.188 / % possible all: 18

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6ML2

6ml2


Resolution: 1.683→38.361 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 43.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 2426 5.04 %
Rwork0.2247 --
obs0.2263 48114 68.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.683→38.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 814 9 76 1786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031823
X-RAY DIFFRACTIONf_angle_d0.5252617
X-RAY DIFFRACTIONf_dihedral_angle_d20.972954
X-RAY DIFFRACTIONf_chiral_restr0.031286
X-RAY DIFFRACTIONf_plane_restr0.003193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6832-1.71750.4151200.3527413X-RAY DIFFRACTION10
1.7175-1.75490.3086350.3249618X-RAY DIFFRACTION16
1.7549-1.79570.387320.3246840X-RAY DIFFRACTION21
1.7957-1.84060.3729570.37321129X-RAY DIFFRACTION29
1.8406-1.89040.4527640.34141443X-RAY DIFFRACTION37
1.8904-1.9460.37821010.35481746X-RAY DIFFRACTION45
1.946-2.00880.35061290.35372426X-RAY DIFFRACTION61
2.0088-2.08060.37191930.34543435X-RAY DIFFRACTION89
2.0806-2.16390.35351810.3163729X-RAY DIFFRACTION96
2.1639-2.26240.33382030.31583798X-RAY DIFFRACTION97
2.2624-2.38160.33872010.28213847X-RAY DIFFRACTION98
2.3816-2.53080.29142110.27823721X-RAY DIFFRACTION96
2.5308-2.72620.26451990.27993635X-RAY DIFFRACTION93
2.7262-3.00040.31691900.26733601X-RAY DIFFRACTION93
3.0004-3.43430.28322100.24163774X-RAY DIFFRACTION97
3.4343-4.3260.22661880.1773818X-RAY DIFFRACTION98
4.326-38.37070.18282120.15843715X-RAY DIFFRACTION95
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)
13.21080.99460.01553.2574-0.74922.9587-0.12920.41490.3961-0.16780.2619-0.5582-0.8508-0.1793-0.0880.4507-0.00470.0520.5664-0.01340.55240.057819.55267.5987
23.0834-0.46770.56811.28020.30971.66680.15930.1887-0.59510.0645-0.0030.19730.1635-0.0451-0.16720.37050.038-0.04020.28050.00950.357323.42373.08498.1477
31.1674-0.01130.25291.504-0.71271.0548-0.1653-0.4470.09170.37670.31490.4117-0.2412-0.426-0.18680.3040.0036-0.00420.48550.0710.43858.122118.78267.0685
41.785-0.22110.81762.8627-0.7981.9536-0.01450.16430.0874-0.77080.16440.01330.31330.0597-0.15130.4987-0.1176-0.08740.40970.03870.384813.008327.1721-11.864
53.2239-1.72072.30962.0725-0.88412.5639-0.0170.1887-0.5405-0.49950.20860.6866-0.24420.0734-0.12120.4028-0.0361-0.11510.38740.02220.375711.940414.5036-4.6372
61.50960.54061.93742.6163-0.75384.7262-0.059-0.5547-0.09850.51310.3307-0.1556-0.2878-0.4086-0.21650.4569-0.0191-0.03990.5792-0.03440.318732.720716.665819.9393
71.55970.45560.24761.6297-0.44433.92610.4021-0.99820.58510.5855-0.0162-0.1430.0233-0.4831-0.23920.6084-0.0776-0.15150.7254-0.15080.461141.44919.814828.8663
82.53040.19161.83611.9810.21913.1752-0.0097-0.2181-0.1802-0.1360.28490.0466-0.1901-0.168-0.3030.4106-0.047-0.0120.3578-0.03530.288925.248916.16110.2235
98.22960.1763.78065.9895-0.38773.8891-0.46891.0629-2.4117-0.74840.79980.5409-0.0520.219-0.43320.533-0.0575-0.1310.5248-0.07560.57899.236310.4509-8.9626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 403 through 428 )
2X-RAY DIFFRACTION2chain 'A' and (resid 429 through 461 )
3X-RAY DIFFRACTION3chain 'A' and (resid 462 through 489 )
4X-RAY DIFFRACTION4chain 'A' and (resid 490 through 514 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 10 )
6X-RAY DIFFRACTION6chain 'E' and (resid 11 through 20 )
7X-RAY DIFFRACTION7chain 'F' and (resid 1 through 5 )
8X-RAY DIFFRACTION8chain 'F' and (resid 6 through 15 )
9X-RAY DIFFRACTION9chain 'F' and (resid 16 through 20 )

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