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- PDB-4ygi: Crystal Structure of SUVH5 SRA bound to fully hydroxymethylated CG DNA -

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Basic information

Entry
Database: PDB / ID: 4ygi
TitleCrystal Structure of SUVH5 SRA bound to fully hydroxymethylated CG DNA
Components
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
  • Polydeoxyribonucleotide
KeywordsTRANSFERASE/DNA / SUVH5 SRA / Fully hydroxymethylated CG / 5-hydroxymethylcytosine / 5hmC binding protein. / TRANSFERASE-DNA complex
Function / homology
Function and homology information


[histone H3]-lysine9 N-methyltransferase / regulatory ncRNA-mediated heterochromatin formation / histone H3K9me2 methyltransferase activity / histone methyltransferase activity / chromosome, centromeric region / epigenetic regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / 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. ...: / 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 motif / Pre-SET domain / 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 / SET domain superfamily / SET domain profile. / SET domain / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsRajakumara, E.
CitationJournal: Sci Rep / Year: 2016
Title: Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain
Authors: Rajakumara, E. / Nakarakanti, N.K. / Nivya, M.A. / Satish, M.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
B: Polydeoxyribonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9675
Polymers21,8942
Non-polymers733
Water28816
1
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
B: Polydeoxyribonucleotide
hetero molecules

A: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5
B: Polydeoxyribonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,93410
Polymers43,7884
Non-polymers1466
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5010 Å2
ΔGint-41 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.980, 76.980, 72.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5 / 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.: 1 / Fragment: SUVH5 SRA DOMAIN, UNP residues 362-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUVH5, SDG9, SET9, At2g35160, T4C15.17 / Plasmid: PETSUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Rosetta2 DE3
References: UniProt: O82175, histone-lysine N-methyltransferase
#2: DNA chain Polydeoxyribonucleotide


Mass: 3378.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium chloride, 0.1M BIS-TRIS pH 6.5, 25%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0718 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 7060 / % possible obs: 98.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 70.4 Å2 / Rmerge(I) obs: 0.066 / Χ2: 2.579 / Net I/av σ(I): 35.506 / Net I/σ(I): 21.7 / Num. measured all: 32545
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.6-2.694.70.752.46821.93199.1
2.69-2.84.80.5726801.72499
2.8-2.934.80.3877011.76199.9
2.93-3.084.80.266951.90799.9
3.08-3.284.80.1327002.30499.6
3.28-3.534.60.0857002.89399.3
3.53-3.884.60.0667003.13999.3
3.88-4.454.50.0547073.56199
4.45-5.64.30.0497263.84898.1
5.6-504.10.0357692.95795.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q0B

3q0b


Resolution: 2.6→33.956 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 331 4.7 %Random
Rwork0.2345 6708 --
obs0.2367 7039 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.93 Å2 / Biso mean: 68.383 Å2 / Biso min: 44.57 Å2
Refinement stepCycle: final / Resolution: 2.6→33.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 204 207 16 1560
Biso mean--63.99 68.1 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031381
X-RAY DIFFRACTIONf_angle_d0.6071910
X-RAY DIFFRACTIONf_chiral_restr0.024211
X-RAY DIFFRACTIONf_plane_restr0.003215
X-RAY DIFFRACTIONf_dihedral_angle_d17.28515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5956-3.26980.39051720.29793278345099
3.2698-33.95860.25441590.21883430358998

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