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- PDB-5wcg: SET and MYND Domain Containing protein 2 -

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Basic information

Entry
Database: PDB / ID: 5wcg
TitleSET and MYND Domain Containing protein 2
ComponentsN-lysine methyltransferase SMYD2
KeywordsTRANSFERASE / Zinc Finger / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / heart development / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / nucleoplasm / 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 (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...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 (Su(var)3-9, Enhancer-of-zeste, Trithorax) 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
Chem-A4M / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsDong, A. / Zeng, H. / Walker, J.R. / Hutch, A. / Seitova, A. / Tatlock, J. / Kumpf, R. / Owen, A. / Taylor, A. / Casimiro-Garcia, A. ...Dong, A. / Zeng, H. / Walker, J.R. / Hutch, A. / Seitova, A. / Tatlock, J. / Kumpf, R. / Owen, A. / Taylor, A. / Casimiro-Garcia, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: The crystal structure of SMYD2 in complex with compound MTF003
Authors: Zeng, H. / Dong, A. / Walker, J.R. / Hutch, A. / Seitova, A. / Tatlock, J. / Kumpf, R. / Owen, A. / Taylor, A. / Casimiro-Garcia, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H.
History
DepositionJun 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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
A: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,73512
Polymers49,8321
Non-polymers90311
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint5 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.343, 98.312, 58.833
Angle α, β, γ (deg.)90.000, 101.950, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

21A-771-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-lysine methyltransferase SMYD2 / HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain- ...HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain-containing protein 2


Mass: 49832.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: unidentified baculovirus
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

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Non-polymers , 6 types, 196 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A4M / [3-(6-amino-2-methyl-9H-purin-9-yl)azetidin-1-yl]{5-[(4-cycloheptylpiperazin-1-yl)methyl]-1-methyl-1H-pyrazol-3-yl}methanone


Mass: 506.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H38N10O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.62 Å3/Da / Density % sol: 53.08 % / Mosaicity: 0.8 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 20% PEG 3350, 0.04M Citric acid, 0.06M Bis-Tris propane pH6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 33305 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.071 / Rrim(I) all: 0.155 / Χ2: 1.513 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.02-2.054.50.98416470.640.5140.837100
2.05-2.094.70.8240.6770.4230.8631000.929
2.09-2.134.90.710.7890.3540.8941000.795
2.13-2.1850.6410.7990.3160.9231000.717
2.18-2.2250.570.8340.2780.9431000.635
2.22-2.2750.4780.8660.2350.9771000.534
2.27-2.3350.4130.90.2020.9441000.461
2.33-2.3950.3570.9280.1740.981000.398
2.39-2.4750.3210.9390.1571.0191000.358
2.47-2.5450.2750.9460.1341.0461000.306
2.54-2.6450.2320.9620.1141.1061000.259
2.64-2.7450.1980.9690.0971.1871000.22
2.74-2.8750.1530.9810.0751.2831000.171
2.87-3.0250.1320.9870.0641.4171000.147
3.02-3.2150.1110.9890.0541.78699.90.124
3.21-3.4550.0940.9910.0462.27999.80.105
3.45-3.84.90.0840.9920.0412.90199.90.094
3.8-4.354.80.0690.9950.0343.14899.80.077
4.35-5.484.80.060.9960.0292.76799.90.067
5.48-504.80.0550.9980.0273.02499.70.061

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.02 Å49.16 Å
Translation2.02 Å49.16 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.7phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S7B

3s7b


Resolution: 2.02→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.205 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.148
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 995 3 %RANDOM
Rwork0.1695 ---
obs0.1708 32306 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.46 Å2 / Biso mean: 27.487 Å2 / Biso min: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å20.76 Å2
2--0.24 Å20 Å2
3----1.1 Å2
Refinement stepCycle: final / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 57 187 3637
Biso mean--24.03 32.99 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193591
X-RAY DIFFRACTIONr_bond_other_d0.0010.023253
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9634873
X-RAY DIFFRACTIONr_angle_other_deg0.96337572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7695448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97924.286161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72815619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4161519
X-RAY DIFFRACTIONr_chiral_restr0.0880.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02717
LS refinement shellResolution: 2.023→2.075 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 67 -
Rwork0.238 2144 -
all-2211 -
obs--90.1 %

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