3JR4	Lyase Dna	date	Sep 08, 2009
title	Mutm Interrogating An Extrahelical G
authors	Y.Qi, M.C.Spong, G.L.Verdine
compound		source
Molecule: Dna Glycosylase Chain: A Fragment: Mutm Ec: 4.2.99.18 Engineered: Yes Mutation: Yes		Organism_scientific: Geobacillus Stearothermophilus Organism_common: Geobacillus Stearothermophilus Organism_taxid: 1422 Gene: Mutm Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet24b
Molecule: Dna (5'-D(Apgpgptpapgpapcpcptpgpgpap 3'); Chain: B Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Tpgcpgptpcpcpap(Gx1) Pgptpcptpapcpc)-3'); Chain: C Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 21 21 21	R_factor 0.190 R_Free 0.237
crystal cell	length a length b length c angle alpha angle beta angle gamma 45.343 95.377 102.482 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.60 Å
ligand	GX1, ZN	enzyme	Lyase E.C.4.2.99.18 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM., Qi Y, Spong MC, Nam K, Karplus M, Verdine GL, J Biol Chem. 2009 Nov 4. PMID:19889642

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk] Biological Unit Coordinates (3jr4.pdb1.gz) 52 Kb LPC: Ligand-Protein Contacts for 3JR4 CSU: Contacts of Structural Units for 3JR4 Structure Factors (100 Kb) Retrieve 3JR4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3JR4 from S2C, [Save to disk] Re-refined 3jr4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3JR4 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 3JR4

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 3JR4, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3jr4_B] [3jr4] [3jr4_C] [3jr4_A] SWISS-PROT database: [P84131] Domain organization of [P84131_BACST] by SWISSPFAM Domains found in 3JR4: [Fapy_DNA_glyco] [H2TH ] by SMART

Other resources with information on 3JR4

Community annotation for 3JR4 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---