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- PDB-4bup: A novel route to product specificity in the Suv4-20 family of his... -

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Basic information

Entry
Database: PDB / ID: 4bup
TitleA novel route to product specificity in the Suv4-20 family of histone H4K20 methyltransferases
ComponentsHISTONE-LYSINE N-METHYLTRANSFERASE SUV420H1
KeywordsTRANSFERASE / EPIGENETICS / HISTONE
Function / homology
Function and homology information


: / condensed chromosome, centromeric region => GO:0000779 / : / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / [histone H4]-lysine20 N-methyltransferase / : / histone H4K20 methyltransferase activity / PKMTs methylate histone lysines / positive regulation of isotype switching / S-adenosyl-L-methionine binding ...: / condensed chromosome, centromeric region => GO:0000779 / : / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / [histone H4]-lysine20 N-methyltransferase / : / histone H4K20 methyltransferase activity / PKMTs methylate histone lysines / positive regulation of isotype switching / S-adenosyl-L-methionine binding / muscle organ development / positive regulation of double-strand break repair via nonhomologous end joining / DNA repair / chromatin binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. ...Histone-lysine N-methyltransferase / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain / Beta Complex / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase KMT5B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.166 Å
AuthorsSouthall, S.M. / Cronin, N.B. / Wilson, J.R.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: A Novel Route to Product Specificity in the Suv4-20 Family of Histone H4K20 Methyltransferases.
Authors: Southall, S.M. / Cronin, N.B. / Wilson, J.R.
History
DepositionJun 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H1
B: HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4837
Polymers62,4632
Non-polymers1,0205
Water3,567198
1
A: HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7874
Polymers31,2311
Non-polymers5563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6953
Polymers31,2311
Non-polymers4642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.310, 50.010, 129.400
Angle α, β, γ (deg.)90.00, 92.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H1 / SUPPRESSOR OF VARIEGATION 4-20 HOMOLOG 1 / SU(VAR)4-20 HOMOLOG 1 / SUV4-20H1


Mass: 31231.396 Da / Num. of mol.: 2 / Fragment: SET DOMAIN, RESIDUES 70-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RIL
References: UniProt: Q3U8K7, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.44 Å3/Da / Density % sol: 49.55 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES, 10 % PEG 10K, pH 7.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→46.6 Å / Num. obs: 28977 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 26.26 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 2.17→2.24 Å / Redundancy: 6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.1 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AU7

4au7


Resolution: 2.166→46.64 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1460 5 %
Rwork0.198 --
obs0.2012 28969 90.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 2.166→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 62 198 3995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073869
X-RAY DIFFRACTIONf_angle_d1.1135194
X-RAY DIFFRACTIONf_dihedral_angle_d16.881448
X-RAY DIFFRACTIONf_chiral_restr0.081545
X-RAY DIFFRACTIONf_plane_restr0.004672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.166-2.24340.28761440.21032704X-RAY DIFFRACTION90
2.2434-2.33320.3021560.20992714X-RAY DIFFRACTION90
2.3332-2.43940.26931360.20812572X-RAY DIFFRACTION85
2.4394-2.5680.29391200.20782510X-RAY DIFFRACTION84
2.568-2.72890.31791340.21892958X-RAY DIFFRACTION97
2.7289-2.93960.28351380.21272916X-RAY DIFFRACTION96
2.9396-3.23530.25971710.21382832X-RAY DIFFRACTION95
3.2353-3.70330.25881390.19392552X-RAY DIFFRACTION85
3.7033-4.66510.23131490.16942970X-RAY DIFFRACTION96
4.6651-46.65090.23181730.1972781X-RAY DIFFRACTION90

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