3F8I Ligase Dna date Nov 12, 2008
title Mouse Uhrf1 Sra Domain Bound With Hemi-Methylated Cpg, Crystal Structure In Space Group P21
authors H.Hashimoto, J.R.Horton, X.Zhang, X.Cheng
compound source
Molecule: E3 Ubiquitin-Protein Ligase Uhrf1
Chain: A, B
Fragment: Ydg Domain: Unp Residues 419-628
Synonym: Ubiquitin-Like Phd And Ring Finger Domain- Containing Protein 1, Ubiquitin-Like-Containing Phd And Ring Finger Domains Protein 1, Nuclear Zinc Finger Protein Np95, Nuclear Protein 95;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_taxid: 10090
Gene: Uhrf1, Np95
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pxc666

Molecule: 5'-D(Dcpdcpdapdtpdgp(5cm) Pdgpdcpdtpdgpdapdc)-3';
Chain: D, F
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna Oligo

Molecule: 5'- D(Dgpdtpdcpdapdgpdcpdgpdcpdapdtpdgpdg)-3';
Chain: E, G
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna Oligo
symmetry Space Group: P 1 21 1
R_factor 0.223 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.084 62.416 113.447 90.00 98.92 90.00
method X-Ray Diffractionresolution 2.29 Å
ligand 5CM enzyme Ligase E.C.6.3.2 BRENDA
Primary referenceUHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications., Hashimoto H, Horton JR, Zhang X, Cheng X, Epigenetics. 2009 Jan 10;4(1). PMID:19077538
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (3f8i.pdb1.gz) 45 Kb
  • Biological Unit Coordinates (3f8i.pdb2.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 3F8I
  • CSU: Contacts of Structural Units for 3F8I
  • Likely Quarternary Molecular Structure file(s) for 3F8I
  • Structure Factors (457 Kb)
  • Retrieve 3F8I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F8I from S2C, [Save to disk]
  • Re-refined 3f8i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F8I 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 3F8I
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3F8I, from MSDmotif at EBI
  • Fold representative 3f8i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f8i_G] [3f8i_A] [3f8i_E] [3f8i_D] [3f8i_B] [3f8i_F] [3f8i]
  • SWISS-PROT database: [Q8VDF2]
  • Domain organization of [UHRF1_MOUSE] by SWISSPFAM
  • Domain found in 3F8I: [SRA ] by SMART
  • Other resources with information on 3F8I
  • Community annotation for 3F8I 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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