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- PDB-6ml4: BTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 3) -

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Basic information

Entry
Database: PDB / ID: 6ml4
TitleBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 3)
Components
  • DNA (5'-D(*AP*CP*GP*CP*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*CP*GP*AP*AP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*TP*TP*CP*GP*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


regulation of immune system process / hematopoietic progenitor cell differentiation / regulation of cytokine production / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding
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 / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / 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 / MOLECULAR REPLACEMENT / Resolution: 1.482 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*CP*GP*AP*AP*GP*C)-3')
F: DNA (5'-D(*TP*GP*CP*TP*TP*CP*GP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,05811
Polymers29,5453
Non-polymers5138
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-38 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.277, 68.807, 48.434
Angle α, β, γ (deg.)90.00, 92.40, 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*CP*GP*AP*AP*GP*C)-3')


Mass: 6168.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(*TP*GP*CP*TP*TP*CP*GP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')


Mass: 6101.928 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 3 types, 361 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.1 M HEPES, pH 7.5, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: PIXEL / Date: Jul 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.48→28.04 Å / Num. obs: 40443 / % possible obs: 80.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.019 / Net I/σ(I): 16.7
Reflection shellResolution: 1.48→1.54 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 570 / CC1/2: 0.53 / Rpim(I) all: 0.53 / % possible all: 11.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6ML3

6ml3


Resolution: 1.482→28.039 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.98
RfactorNum. reflection% reflection
Rfree0.2113 1981 4.91 %
Rwork0.1907 --
obs0.1917 40368 80.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.482→28.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1131 814 17 353 2315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032106
X-RAY DIFFRACTIONf_angle_d0.5322996
X-RAY DIFFRACTIONf_dihedral_angle_d24.423845
X-RAY DIFFRACTIONf_chiral_restr0.045321
X-RAY DIFFRACTIONf_plane_restr0.003243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4824-1.51940.3499150.3781267X-RAY DIFFRACTION8
1.5194-1.56050.4428350.316819X-RAY DIFFRACTION24
1.5605-1.60640.2881800.27211382X-RAY DIFFRACTION41
1.6064-1.65830.27281070.25832078X-RAY DIFFRACTION61
1.6583-1.71750.2391720.24653031X-RAY DIFFRACTION90
1.7175-1.78630.26891670.2433404X-RAY DIFFRACTION100
1.7863-1.86760.25641810.22643420X-RAY DIFFRACTION100
1.8676-1.9660.25441710.21823375X-RAY DIFFRACTION100
1.966-2.08910.23631830.20773424X-RAY DIFFRACTION100
2.0891-2.25040.19421750.20463409X-RAY DIFFRACTION100
2.2504-2.47670.2091800.19533413X-RAY DIFFRACTION100
2.4767-2.83480.19061730.19183430X-RAY DIFFRACTION100
2.8348-3.57040.19911650.17633439X-RAY DIFFRACTION99
3.5704-28.04450.17891770.14333496X-RAY DIFFRACTION100
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)
19.9331-1.01095.52244.2879-3.38397.81070.11230.13270.1656-0.1725-0.3022-0.15160.4215-0.05870.23180.24420.06680.05780.2309-0.07060.218636.197435.812328.8499
28.2635-1.8280.47719.09842.5795.87930.02010.3039-0.0119-0.4801-0.0887-0.60170.59880.4890.07140.3240.09090.09850.20640.0140.2140.691633.174522.3183
34.7326-2.2687-2.87177.32272.15124.83960.11160.14760.4894-0.41350.1254-0.2129-0.65970.0188-0.20290.1373-0.03110.02270.16680.02280.194941.550924.89057.9771
40.5387-1.018-0.87454.78423.80243.03-0.15840.1478-0.2326-0.0350.0991-0.13850.3261-0.12720.00650.1297-0.02320.04970.2077-0.01910.108938.728715.0537.3696
56.7950.5959-0.73864.98990.80722.12320.0147-0.081-0.24590.18350.076-0.03910.05720.0893-0.08510.12390.0241-0.01920.07490.00970.063625.5782.5387.1451
62.8266-0.0659-0.51063.604-3.04582.7604-0.0285-0.1753-0.00030.17560.10780.1425-0.1567-0.0741-0.08790.0956-0.0020.01010.1048-0.02250.0788.774416.53557.9213
75.8289-1.06171.66524.8558-1.7378.5005-0.12490.4045-0.0961-0.56660.12110.1810.29840.07070.05430.1568-0.0534-0.01350.1117-0.01710.139312.978627.1905-11.0536
83.6492-1.47983.96790.6359-1.28757.6243-0.03090.30780.0627-0.38430.10650.1933-0.09610.2745-0.03230.2296-0.0601-0.06240.16480.01470.15496.34318.5954-10.5388
96.8393-5.05066.34126.1435-3.48736.4441-0.0134-0.0377-0.4073-0.1530.18730.3693-0.2067-0.0716-0.20980.15480.0030.0050.085-0.00420.076617.754110.64031.1344
103.57820.08311.75932.131-0.12755.98460.0511-0.5748-0.03360.26590.175-0.1045-0.0123-0.4178-0.16860.136-0.0123-0.00860.1779-0.02430.103633.332217.024519.7061
114.23280.7872.86792.43861.04525.3260.0019-0.3713-0.02990.31270.1202-0.1857-0.12730.0028-0.11030.16210.0114-0.0190.1922-0.02240.097636.200616.46122.8661
124.82910.81473.80296.88941.5833.1186-0.07880.13220.1047-0.49990.2481-0.1313-1.1191-0.346-0.21120.2323-0.00970.00120.15670.03480.114121.312319.41982.8824
135.5308-0.95443.65636.9047-0.14767.296-0.42151.0737-1.8474-0.55390.83840.16860.24710.1431-0.49420.2688-0.0512-0.05160.2351-0.07080.29999.410410.3677-8.8258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 374 through 388 )
2X-RAY DIFFRACTION2chain 'A' and (resid 389 through 399 )
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 416 )
4X-RAY DIFFRACTION4chain 'A' and (resid 417 through 428 )
5X-RAY DIFFRACTION5chain 'A' and (resid 429 through 456 )
6X-RAY DIFFRACTION6chain 'A' and (resid 457 through 489 )
7X-RAY DIFFRACTION7chain 'A' and (resid 490 through 514 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 5 )
9X-RAY DIFFRACTION9chain 'E' and (resid 6 through 10 )
10X-RAY DIFFRACTION10chain 'E' and (resid 11 through 20 )
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 10 )
12X-RAY DIFFRACTION12chain 'F' and (resid 11 through 15 )
13X-RAY DIFFRACTION13chain 'F' and (resid 16 through 20 )

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