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- PDB-5kch: SETDB1 in complex with an early stage, low affinity fragment cand... -

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Basic information

Entry
Database: PDB / ID: 5kch
TitleSETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy into weak electron density
ComponentsHistone-lysine N-methyltransferase SETDB1
KeywordsTRANSFERASE / Fragment Screening / DIAMOND I04-1 XCHEM / PANDDA / Structural Genomics / Structural Genomics Consortium / SGC
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
4-methoxy-N-[(pyridin-2-yl)methyl]aniline / Histone-lysine N-methyltransferase SETDB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsTempel, W. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Walker, J.R. / Brown, P.J. / Schapira, M. / Collins, P. / Pearce, N. / Brandao-Neto, J. ...Tempel, W. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Walker, J.R. / Brown, P.J. / Schapira, M. / Collins, P. / Pearce, N. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Santhakumar, V. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy
Authors: Tempel, W. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Walker, J.R. / Brown, P.J. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Santhakumar, S. / Structural Genomics Consortium (SGC)
History
DepositionJun 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Structure summary
Revision 2.0Feb 20, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Sep 27, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,94055
Polymers26,3371
Non-polymers16,60254
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.967, 63.607, 70.457
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: 26337.348 Da / Num. of mol.: 1 / Fragment: UNP residues 196-403
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 , 5 types, 169 molecules

#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 322.358 Da / Num. of mol.: 50 / Source method: obtained synthetically
#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.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-6RN / 4-methoxy-N-[(pyridin-2-yl)methyl]aniline


Mass: 214.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
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: DECTRIS PILATUS 6M-F / 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: 1.7→43.82 Å / Num. obs: 28318 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 21.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Net I/σ(I): 10.5 / Num. measured all: 176868
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.736.31.1511.4937514780.6710.4941.255100
9-43.825.80.0533.513792390.9960.0230.05699.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.26data scaling
PDB_EXTRACT3.2data extraction
xia2data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KCO

5kco


Resolution: 1.7→43.82 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.75
Details: Users of this crystal structure: verify our intepretion of the electron density. Amplitudes and unmerged intensities are included with this deposition. Diffraction images will be deposited ...Details: Users of this crystal structure: verify our intepretion of the electron density. Amplitudes and unmerged intensities are included with this deposition. Diffraction images will be deposited in a public repository. Geometry restraints for the fragment candidate were prepared with GRADE and modified by removal of plane restraints for atoms {C11, C4, N, C5} and atoms {N, C4, C5, H5}. The methyl group of the fragment candidate was not resolved by electron density and was omitted from the model. Ambiguous difference density suggests more than one main chain conformation for residues 235..239.
RfactorNum. reflection% reflection
Rfree0.2575 1440 5.1 %
Rwork0.215 --
obs0.2171 28258 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.71 Å2 / Biso mean: 25.14 Å2 / Biso min: 11.34 Å2
Refinement stepCycle: final / Resolution: 1.7→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 79 115 1878
Biso mean--29.9 30.25 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131797
X-RAY DIFFRACTIONf_angle_d1.0792455
X-RAY DIFFRACTIONf_chiral_restr0.081264
X-RAY DIFFRACTIONf_plane_restr0.007320
X-RAY DIFFRACTIONf_dihedral_angle_d11.2421068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.76080.32341480.275226242772
1.7608-1.83130.3311350.258426402775
1.8313-1.91460.28651370.233126582795
1.9146-2.01560.27351550.23326392794
2.0156-2.14180.29411360.251926552791
2.1418-2.30720.31261560.265826372793
2.3072-2.53940.30421310.257126912822
2.5394-2.90680.29391510.228426902841
2.9068-3.66190.23021420.18627302872
3.6619-43.83810.19631490.174328543003
Refinement TLS params.Method: refined / Origin x: 24.3406 Å / Origin y: 63.5815 Å / Origin z: 7.5794 Å
111213212223313233
T0.1514 Å20.0024 Å2-0.0125 Å2-0.1453 Å2-0.0097 Å2--0.1451 Å2
L0.453 °20.4758 °2-0.4058 °2-0.8759 °2-0.5743 °2--0.7319 °2
S-0.0468 Å °-0.0195 Å °-0.0404 Å °-0.0674 Å °0.0105 Å °-0.0129 Å °0.0912 Å °-0.0118 Å °-0 Å °
Refinement TLS groupSelection details: chain A

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