3Q0C Transferase Dna date Dec 15, 2010
title Crystal Structure Of Suvh5 Sra-Fully Methylated Cg Dna Compl Space Group P6122
authors R.Eerappa, D.K.Simanshu, D.J.Patel
compound source
Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-9 S Suvh5;
Chain: X, A
Fragment: Suvh5 Sra Domain (Unp Residues 362-528)
Synonym: Histone H3-K9 Methyltransferase 5, H3-K9-Hmtase 5, Set Domain Group 9, Suppressor Of Variegation 3-9 Homolog P Su(Var)3-9 Homolog Protein 5;
Ec: 2.1.1.43
Engineered: Yes
 Organism_scientific: Arabidopsis Thaliana
Organism_common: Mouse-Ear Cress,Thale-Cress
Organism_taxid: 3702
Gene: At2g35160, Sdg9, Set9, Suvh5, T4c15.17
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Rosetta2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet Sumo

Molecule: Dna (5'-D(Apcptpap(5cm)Pgptpapgptpt)-3
Chain: C, B
Engineered: Yes
Other_details: Self Complementary Fully Methylated Cg Dna
Synthetic: Yes
Other_details: Chemically Synthesized
symmetry Space Group: P 61 2 2
R_factor 0.251 R_Free 0.303
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.462 104.462 176.691 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.66 Å
ligand 5CM, MG enzyme Transferase E.C.2.1.1.43 BRENDA
Primary referenceA dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo., Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE, Genes Dev. 2011 Jan 15;25(2):137-52. PMID:21245167
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk]
  • Biological Unit Coordinates (3q0c.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 3Q0C
  • CSU: Contacts of Structural Units for 3Q0C
  • Structure Factors (128 Kb)
  • Retrieve 3Q0C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3Q0C from S2C, [Save to disk]
  • Re-refined 3q0c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3Q0C in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3Q0C
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3Q0C, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3q0c_A] [3q0c_X] [3q0c] [3q0c_C] [3q0c_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3Q0C: [SRA ] by SMART
    • Other resources with information on 3Q0C
  • Community annotation for 3Q0C at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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