3M4A	Isomerase Dna	date	Mar 10, 2010
title	Crystal Structure Of A Bacterial Topoisomerase Ib In Complex Reveals A Secondary Dna Binding Site
authors	A.Patel, L.Yakovleva, S.Shuman, A.Mondragon
compound		source
Molecule: Putative Type I Topoisomerase Chain: A Engineered: Yes		Organism_scientific: Deinococcus Radiodurans Organism_taxid: 1299 Gene: Dr_0690 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21b
Molecule: Dna (5'-D(Gpapaptpapapgpgpgpcpgpc)-3' Chain: D Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Gpcpgpcpcpcptptpaptptpc)-3' Chain: E Engineered: Yes		Synthetic: Yes
symmetry	Space Group: C 1 2 1	R_factor 0.193 R_Free 0.222
crystal cell	length a length b length c angle alpha angle beta angle gamma 119.670 53.440 77.360 90.00 96.33 90.00
method	X-Ray Diffraction	resolution	1.65 Å
ligand	ACY, MG	enzyme
Gene	DR
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site., Patel A, Yakovleva L, Shuman S, Mondragon A, Structure. 2010 Jun 9;18(6):725-33. PMID:20541510

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk] Biological Unit Coordinates (3m4a.pdb1.gz) 64 Kb LPC: Ligand-Protein Contacts for 3M4A CSU: Contacts of Structural Units for 3M4A Structure Factors (420 Kb) Retrieve 3M4A in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3M4A from S2C, [Save to disk] Re-refined 3m4a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3M4A 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 3M4A

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 3M4A, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3m4a_E] [3m4a_D] [3m4a_A] [3m4a] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3M4A

Community annotation for 3M4A at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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