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- PDB-5kh6: SETDB1 in complex with a fragment candidate -

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Basic information

Entry
Database: PDB / ID: 5kh6
TitleSETDB1 in complex with a fragment candidate
ComponentsHistone-lysine N-methyltransferase SETDB1
KeywordsTRANSFERASE / FRAGMENT SCREENING / STRUCTURAL GENOMICS CONSORTIUM / SGC / DIAMOND I04-1 XCHEM / PANDDA
Function / homology
Function and homology information


[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / transposable element silencing by heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3 methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / transposable element silencing by heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3 methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Regulation of endogenous retroelements by KRAB-ZFP proteins / promoter-specific chromatin binding / PKMTs methylate histone lysines / chromosome / methylation / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / : / : ...Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / : / : / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Tudor domain / Tudor domain / Post-SET domain / Post-SET domain profile. / SH3 type barrels. - #140 / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
methyl 3-(methylsulfonylamino)benzoate / ACETATE ION / DI(HYDROXYETHYL)ETHER / Histone-lysine N-methyltransferase SETDB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsWalker, J.R. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Dong, A. / Collins, P. / Pearce, N. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. ...Walker, J.R. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Dong, A. / Collins, P. / Pearce, N. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Brown, P.J. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Santhakumar, V. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: SETDB1 in complex with a fragment candidate
Authors: Walker, J.R. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Dong, A. / Collins, P. / Pearce, N. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Brown, P.J. / Schapira, M. / ...Authors: Walker, J.R. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Dong, A. / Collins, P. / Pearce, N. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Brown, P.J. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Santhakumar, V. / Structural Genomics Consortium (SGC)
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,27521
Polymers24,6271
Non-polymers1,64720
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-57 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.760, 63.810, 70.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone-lysine N-methyltransferase SETDB1 / ERG-associated protein with SET domain / ESET / Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 ...ERG-associated protein with SET domain / ESET / Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 / Lysine N-methyltransferase 1E / SET domain bifurcated 1


Mass: 24627.381 Da / Num. of mol.: 1 / Fragment: Tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, KIAA0067, KMT1E / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus
References: UniProt: Q15047, histone-lysine N-methyltransferase

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Non-polymers , 9 types, 177 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-6SU / methyl 3-(methylsulfonylamino)benzoate


Mass: 229.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO4S
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG-3350, 0.2M lithium sulfate, 0.1M bis-tris. Trypsin had been added to the protein stock solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.87→27.69 Å / Num. obs: 21344 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.058 / Rrim(I) all: 0.149 / Net I/σ(I): 10.1 / Num. measured all: 137998
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.87-1.916.81.536199.9
8.97-27.695.50.028196.7

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
autoXDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: isomorphous crystal stucture of SETDB1 in complex with a different fragment candidate

Resolution: 2.05→27.69 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.502 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.235 501 3.08 %RANDOM
Rwork0.178 ---
obs0.18 16266 99.8 %-
Displacement parametersBiso max: 114.42 Å2 / Biso mean: 32.94 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1--5.851 Å20 Å20 Å2
2--11.7849 Å20 Å2
3----5.9339 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.05→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 95 160 1968
Biso mean--62.35 42.61 -
Num. residues----211
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d815SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes529HARMONIC5
X-RAY DIFFRACTIONt_it3677HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion227SEMIHARMONIC5
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_contact3634SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3677HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6603HARMONIC40.72
X-RAY DIFFRACTIONt_omega_torsion4.57
X-RAY DIFFRACTIONt_other_torsion14.28
LS refinement shellResolution: 2.05→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.226 89 3.07 %
Rwork0.173 2812 -
all-2901 -
obs--100 %
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)
12.21112.1972-0.64834.5259-0.69681.6131-0.15680.1128-0.1555-0.29820.0508-0.27270.14970.08370.106-0.06150.01590.03410.0803-0.011-0.060240.150869.2421-3.0795
22.08940.4485-0.3171.1405-0.84521.94420.0009-0.09990.0360.0472-0.00530.03940.0731-0.04690.0044-0.09350.0127-0.00530.017-0.0143-0.116222.893867.12919.1986
31.57650.06650.59435.5004-0.06664.06590.10390.0463-0.1029-0.36850.05880.19170.21350.1209-0.1627-0.046-0.0105-0.01120.0948-0.0075-0.084810.180551.8915.8939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|190 - 248 }A190 - 248
2X-RAY DIFFRACTION2{ A|249 - 345 }A249 - 345
3X-RAY DIFFRACTION3{ A|346 - 400 }A346 - 400

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