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- PDB-3qkj: The PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BE... -

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Basic information

Entry
Database: PDB / ID: 3qkj
TitleThe PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BETA in complex with a bis-tris molecule
ComponentsDNA cytosine-5 methyltransferase 3 beta isoform 6 variant
KeywordsTRANSFERASE / DNMT3B / PWWP DOMAIN / METHYLTRANSFERASE 3 BETA / SGC / S-ADENOSYL-L-METHIONINE / ZINC-FINGER / Structural Genomics / Structural Genomics Consortium
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 ...: / 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 / methyltransferase activity / 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 / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / : / DNMT3, ADD PHD zinc finger / 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 / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site ...PWWP, helical domain / DNA (cytosine-5)-methyltransferase 3B, ADD domain / : / DNMT3, ADD PHD zinc finger / 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 / 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
DNA cytosine-5 methyltransferase 3 beta isoform 6 variant / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsZeng, H. / Amaya, M.F. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2011
Title: Structural and Histone Binding Ability Characterizations of Human PWWP Domains.
Authors: Wu, H. / Zeng, H. / Lam, R. / Tempel, W. / Amaya, M.F. / Xu, C. / Dombrovski, L. / Qiu, W. / Wang, Y. / Min, J.
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: DNA cytosine-5 methyltransferase 3 beta isoform 6 variant
B: DNA cytosine-5 methyltransferase 3 beta isoform 6 variant
C: DNA cytosine-5 methyltransferase 3 beta isoform 6 variant
D: DNA cytosine-5 methyltransferase 3 beta isoform 6 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,43714
Polymers67,0244
Non-polymers1,41310
Water4,738263
1
A: DNA cytosine-5 methyltransferase 3 beta isoform 6 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1574
Polymers16,7561
Non-polymers4013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA cytosine-5 methyltransferase 3 beta isoform 6 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1574
Polymers16,7561
Non-polymers4013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA cytosine-5 methyltransferase 3 beta isoform 6 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9652
Polymers16,7561
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA cytosine-5 methyltransferase 3 beta isoform 6 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1574
Polymers16,7561
Non-polymers4013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.544, 74.544, 160.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
DNA cytosine-5 methyltransferase 3 beta isoform 6 variant


Mass: 16755.896 Da / Num. of mol.: 4 / Fragment: UNP residues 293-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59H79, UniProt: Q9UBC3*PLUS
#2: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.84 Å3/Da / Density % sol: 67.93 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6
Details: pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 5, 2009
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 62267 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 51.72 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→34.04 Å / Cor.coef. Fo:Fc: 0.9567 / Cor.coef. Fo:Fc free: 0.9454 / SU B: 4.788 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 3163 5.08 %RANDOM
Rwork0.2088 ---
obs0.2098 62267 98.4 %-
all-59117 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.6355 Å20 Å20 Å2
2--0.6355 Å20 Å2
3----1.271 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.04→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 86 263 4455
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014330HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975842HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1405SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes634HARMONIC5
X-RAY DIFFRACTIONt_it4278HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.04→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 213 5.17 %
Rwork0.253 3907 -
all0.253 4120 -
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)
15.08922.5632-0.75242.4553-0.42261.68880.0455-0.21840.0698-0.0313-0.13080.0293-0.07910.01720.0853-0.0927-0.0572-0.0528-0.0298-0.0003-0.08636.70154.143834.2364
25.44462.4279-0.71482.0917-0.26261.7439-0.20030.10020.0979-0.06420.12010.0449-0.0255-0.07870.0801-0.0955-0.0591-0.0211-0.0314-0.0441-0.08489.293738.242130.9742
31.6835-0.69890.15823.64640.35268.21210.3775-0.0693-0.1255-0.6515-0.09820.25520.45240.2191-0.27930.0549-0.0255-0.0474-0.27270.011-0.134141.194276.668414.7812
42.3219-1.01240.10412.66580.14217.7142-0.2953-0.28560.15090.34080.5898-0.21750.44430.2854-0.2945-0.20140.1304-0.0188-0.0031-0.044-0.12662.066545.654150.5457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }0
2X-RAY DIFFRACTION2{ B|* }0
3X-RAY DIFFRACTION3{ C|* }0
4X-RAY DIFFRACTION4{ D|* }0

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