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- PDB-5nrv: Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol -

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Basic information

Entry
Database: PDB / ID: 5nrv
TitleHuman DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol
ComponentsDNA (cytosine-5)-methyltransferase 3B
KeywordsTRANSFERASE / DNMT3B PWWP DOMAIN / HISTONE BINDING / BETA BARREL / LIGAND
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / NoRC negatively regulates rRNA expression ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / NoRC negatively regulates rRNA expression / transcription corepressor activity / methylation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site ...PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
6-dipropylamino-1-hexanol / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.075 Å
AuthorsRondelet, G. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
F.R.S._FNRS_Televie7.4.532.15.F. Belgium
CitationJournal: To be published
Title: Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors
Authors: Rondelet, G. / Dal Maso, T. / Maniquet, A. / Themans, Q. / Wouters, J.
History
DepositionApr 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
D: DNA (cytosine-5)-methyltransferase 3B
A: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,76114
Polymers33,3982
Non-polymers1,36312
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-137 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.550, 73.550, 155.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11D-530-

HOH

21D-607-

HOH

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3B / Dnmt3b / DNA methyltransferase HsaIIIB / M.HsaIIIB


Mass: 16698.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Chemical ChemComp-96K / 6-dipropylamino-1-hexanol


Mass: 201.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H27NO
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.63 Å3/Da / Density % sol: 66.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350 / PH range: 5.7-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2015 / Details: X-RAY FLUORESCCENCE DETECTOR
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL-CUT SI[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.07→40.173 Å / Num. obs: 30107 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 43.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.38
Reflection shellResolution: 2.07→2.21 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 4748 / CC1/2: 0.862 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QKJ

3qkj


Resolution: 2.075→40.173 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.95
RfactorNum. reflection% reflection
Rfree0.2435 1506 5 %
Rwork0.2071 --
obs0.2089 30106 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.24 Å2 / Biso mean: 38.52 Å2 / Biso min: 17.52 Å2
Refinement stepCycle: final / Resolution: 2.075→40.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 78 183 2348
Biso mean--43.58 45.95 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072216
X-RAY DIFFRACTIONf_angle_d1.0972974
X-RAY DIFFRACTIONf_chiral_restr0.077284
X-RAY DIFFRACTIONf_plane_restr0.004357
X-RAY DIFFRACTIONf_dihedral_angle_d13.615794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0751-2.14210.29671310.27072493262497
2.1421-2.21870.2941350.260825572692100
2.2187-2.30750.27651380.236525742712100
2.3075-2.41250.26681320.251325612693100
2.4125-2.53970.3071370.241626012738100
2.5397-2.69870.26231350.222825622697100
2.6987-2.90710.26461380.220525962734100
2.9071-3.19950.22791370.21626232760100
3.1995-3.66220.23461370.19726162753100
3.6622-4.61290.22251400.172426442784100
4.6129-40.18020.23471460.20542773291999

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