regulatory ncRNA-mediated heterochromatin formation / [histone H3]-lysine9 N-methyltransferase / histone H3K9me2 methyltransferase activity / histone methyltransferase activity / chromosome, centromeric region / epigenetic regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / double-stranded DNA binding / zinc ion binding / nucleus Similarity search - Function
Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / PUA domain-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Pre-SET domain ...Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / PUA domain-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / PUA-like superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Roll / Mainly Beta Similarity search - Domain/homology
Histone-lysineN-methyltransferase, H3lysine-9specificSUVH5 / Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Protein SET DOMAIN GROUP 9 / Suppressor of ...Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Protein SET DOMAIN GROUP 9 / Suppressor of variegation 3-9 homolog protein 5 / Su(var)3-9 homolog protein 5
Mass: 18515.920 Da / Num. of mol.: 2 / Fragment: SUVH5 SRA Domain (UNP Residues 362-528) Source method: isolated from a genetically manipulated source Details: Cleavable N-terminal His-SUmo tag / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g35160, SDG9, SET9, SUVH5, T4C15.17 / Plasmid: pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) References: UniProt: O82175, histone-lysine N-methyltransferase
#2: DNA chain
DNA (5'-D(*TP*CP*CP*AP*(5CM)P*GP*TP*CP*AP*G)-3')
Mass: 3019.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: DNA chain
DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*GP*A)-3')
Mass: 3085.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 19% PEG4000, 100 mM MES, pH 6.5, 200 mM NaCl and 3 mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Method to determine structure: MOLECULAR REPLACEMENT Starting model: SRA Molecule from the SUVH5 SRA-fully methylated Cg DNA crystallized in space group P42212 Resolution: 2.3704→19.095 Å / SU ML: 0.35 / σ(F): 1.39 / Phase error: 27.86 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2628
873
5.07 %
Rwork
0.2246
-
-
obs
0.2265
17221
98.78 %
Solvent computation
Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.199 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
1.8426 Å2
-0 Å2
0 Å2
2-
-
1.8426 Å2
0 Å2
3-
-
-
-7.7466 Å2
Refinement step
Cycle: LAST / Resolution: 2.3704→19.095 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2173
405
1
51
2630
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
3114
X-RAY DIFFRACTION
f_angle_d
1.378
4382
X-RAY DIFFRACTION
f_dihedral_angle_d
22.458
1195
X-RAY DIFFRACTION
f_chiral_restr
0.082
486
X-RAY DIFFRACTION
f_plane_restr
0.007
433
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
X
966
X-RAY DIFFRACTION
POSITIONAL
1
2
A
966
X-RAY DIFFRACTION
POSITIONAL
0.031
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3704-2.5186
0.3309
135
0.3062
2584
X-RAY DIFFRACTION
94
2.5186-2.7125
0.3171
132
0.2631
2737
X-RAY DIFFRACTION
100
2.7125-2.9846
0.3162
146
0.276
2758
X-RAY DIFFRACTION
100
2.9846-3.4143
0.3028
142
0.2531
2751
X-RAY DIFFRACTION
100
3.4143-4.2936
0.2668
170
0.2141
2738
X-RAY DIFFRACTION
100
4.2936-19.0954
0.2124
148
0.1933
2780
X-RAY DIFFRACTION
99
+
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