3K9F	Isomerase Dna	date	Oct 15, 2009
title	Detailed Structural Insight Into The Quinolone-Dna Cleavage Type Iia Topoisomerases
authors	I.Laponogov, X.S.Pan, D.A.Veselkov, L.M.Fisher, M.R.Sanderson
compound		source
Molecule: Dna Topoisomerase 4 Subunit A Chain: A, B Fragment: Residues 1-488 Synonym: Topoisomerase Iv Subunit A Ec: 5.99.1.- Engineered: Yes		Organism_scientific: Streptococcus Pneumoniae Organism_taxid: 1313 Strain: 7785 Gene: Parc Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet29a
Molecule: Dna Topoisomerase 4 Subunit B Chain: C, D Fragment: Residues 404-647 Synonym: Topoisomerase Iv Subunit B Ec: 5.99.1.- Engineered: Yes		Organism_scientific: Streptococcus Pneumoniae Organism_taxid: 1313 Strain: 7785 Gene: Pare Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet19b
Molecule: Dna (5'-D(Apcpcpapapgpgptcpaptpgpap Chain: E Engineered: Yes Other_details: Dna E Site		Synthetic: Yes
Molecule: Dna (5'- D(Papgptpcpaptptpcpaptpgpapcpcptptpgpgpt Chain: F Engineered: Yes Other_details: Dna E Site		Synthetic: Yes
Molecule: Dna (5'-D(Cptpgptptptptpacpgptpgpcp Chain: G Engineered: Yes Other_details: Dna E Site		Synthetic: Yes
Molecule: Dna (5'- D(Pgpapcptpaptpgpcpapcpgptpapapapapcpapg Chain: H Engineered: Yes Other_details: Dna E Site		Synthetic: Yes
symmetry	Space Group: P 32	R_factor 0.183 R_Free 0.218
crystal cell	length a length b length c angle alpha angle beta angle gamma 122.407 122.407 178.287 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	LFX, MG	enzyme	Isomerase E.C.5.99.1 BRENDA
Gene Ontology	Chain Function Process Component A, B D, C
Primary reference	Structural basis of gate-DNA breakage and resealing by type II topoisomerases., Laponogov I, Pan XS, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR, PLoS One. 2010 Jun 28;5(6):e11338. PMID:20596531

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (500 Kb) [Save to disk] Biological Unit Coordinates (3k9f.pdb1.gz) 487 Kb LPC: Ligand-Protein Contacts for 3K9F CSU: Contacts of Structural Units for 3K9F Structure Factors (496 Kb) Retrieve 3K9F in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3K9F from S2C, [Save to disk] Re-refined 3k9f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3K9F 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 3K9F

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3K9F, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3k9f] [3k9f_G] [3k9f_E] [3k9f_C] [3k9f_B] [3k9f_A] [3k9f_D] [3k9f_H] [3k9f_F] SWISS-PROT database: [P72525] [Q59961] Domain organization of [PARC_STRPN] [PARE_STRPN] by SWISSPFAM Domains found in 3K9F: [TOP2c] [TOP4c ] by SMART

Other resources with information on 3K9F

Community annotation for 3K9F at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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