6RKW Isomerase date Apr 30, 2019
title Cryoem Structure Of The Complete E. Coli Dna Gyrase Complex 130 Bp Dna Duplex
authors A.Vanden Broeck, V.Lamour
compound source
Molecule: Dna Gyrase Subunit A
Chain: A, C
Ec: 5.6.2.3
Engineered: Yes
Other_details: Gyra Subunit
Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Gene: Gyra, Hisw, Nala, Pard, B2231, Jw2225
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna Gyrase Subunit B
Chain: B, D
Synonym: Type Iia Topoisomerase Subunit Gyrb
Ec: 5.6.2.3
Engineered: Yes
Other_details: Gyrb Subunit

Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Gene: Gyrb, Acrb, Cou, Himb, Hisu, Nalc, Para, Pcba, B3699,
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693

Molecule: Dna (58-Mer)
Chain: F, E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Dna (62-Mer)
Chain: G, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 6.60 Å
ligand ANP, JHN enzyme Isomerase E.C.5.6.2.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceCryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex., Vanden Broeck A, Lotz C, Ortiz J, Lamour V, Nat Commun. 2019 Oct 30;10(1):4935. doi: 10.1038/s41467-019-12914-y. PMID:31666516
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (546 Kb) [Save to disk]
  • Biological Unit Coordinates (6rkw.pdb1.gz) 532 Kb
  • LPC: Ligand-Protein Contacts for 6RKW
  • CSU: Contacts of Structural Units for 6RKW
  • Retrieve 6RKW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6RKW from S2C, [Save to disk]
  • View 6RKW 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 6RKW
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6rkw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6rkw_H] [6rkw_C] [6rkw_A] [6rkw_G] [6rkw_D] [6rkw_B] [6rkw_E] [6rkw_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6RKW
  • Community annotation for 6RKW at PDBWiki (http://pdbwiki.org)

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