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- PDB-3qww: Crystal structure of histone lysine methyltransferase SmyD2 in co... -

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Basic information

Entry
Database: PDB / ID: 3qww
TitleCrystal structure of histone lysine methyltransferase SmyD2 in complex with the methyltransferase inhibitor sinefungin
ComponentsSET and MYND domain-containing protein 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Methyltransferase / Hsp90 / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Regulation of TP53 Activity through Methylation / [histone H3]-lysine4 N-trimethyltransferase / PKMTs methylate histone lysines / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding ...Regulation of TP53 Activity through Methylation / [histone H3]-lysine4 N-trimethyltransferase / PKMTs methylate histone lysines / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding / Transferases; Transferring one-carbon groups; Methyltransferases / p53 binding / heart development / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET domain superfamily / SET domain ...SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
SINEFUNGIN / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsJiang, Y. / Sirinupong, N. / Brunzelle, J. / Yang, Z.
CitationJournal: Plos One / Year: 2011
Title: Crystal structures of histone and p53 methyltransferase SmyD2 reveal a conformational flexibility of the autoinhibitory C-terminal domain.
Authors: Jiang, Y. / Sirinupong, N. / Brunzelle, J. / Yang, Z.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SET and MYND domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2205
Polymers49,6421
Non-polymers5784
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.520, 75.150, 112.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SET and MYND domain-containing protein 2


Mass: 49642.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smyd2 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R5A0
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% polyethylene glycol 8000, 50 mM NaCl, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 46001 / Num. obs: 45863 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 20.93 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4508 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
BUSTER2.8.0refinement
HKL-2000data reduction
SCALEPACKdata scaling
BUSTER2.8.0phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3QWW

3qww


Resolution: 1.8→28.13 Å / Cor.coef. Fo:Fc: 0.9457 / Cor.coef. Fo:Fc free: 0.9215 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 2311 5.05 %RANDOM
Rwork0.1857 ---
all0.1868 45921 --
obs0.1868 45783 --
Displacement parametersBiso mean: 26.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.2063 Å20 Å20 Å2
2--2.5099 Å20 Å2
3----2.3036 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 30 429 3900
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0135732
X-RAY DIFFRACTIONt_angle_deg1.0448242
X-RAY DIFFRACTIONt_dihedral_angle_d12752
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes922
X-RAY DIFFRACTIONt_gen_planes5185
X-RAY DIFFRACTIONt_it357320
X-RAY DIFFRACTIONt_nbd15
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion18.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4495
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_contact44804
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 176 5.37 %
Rwork0.2238 3103 -
all0.2265 3279 -

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