5BS8 Isomerase Dna date Jun 01, 2015
title Crystal Structure Of A Topoisomerase II Complex
authors T.R.Blower, B.H.Williamson, R.J.Kerns, J.M.Berger
compound source
Molecule: Dna Gyrase Subunit A
Chain: A, C
Fragment: Gyra Tower And C-Gate Domains
Ec: 5.99.1.3
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis (Strain Atc H37rv);
Organism_taxid: 83332
Strain: Atcc 25618 H37rv
Gene: Gyra, Rv0006, Mtcy10h4.04
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28b

Molecule: Dna Gyrase Subunit B
Chain: B, D
Fragment: Gyrb Toprim Domain
Ec: 5.99.1.3
Engineered: Yes

Organism_scientific: Mycobacterium Tuberculosis (Strain Atc H37rv);
Organism_taxid: 83332
Strain: Atcc 25618 H37rv
Gene: Gyrb, Rv0005, Mtcy10h4.03
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28b

Molecule: Dna Substrate 24-Mer Ggtcatgaatgactatgcacgtaa
Chain: E, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna Substrate 24-Mer Ttacgtgcatagtcattcatgacc
Chain: F, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.196 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.357 83.070 129.856 90.00 109.33 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand MFX, MG, PTR enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceCrystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis., Blower TR, Williamson BH, Kerns RJ, Berger JM, Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):1706-13. doi:, 10.1073/pnas.1525047113. Epub 2016 Jan 20. PMID:26792525
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (824 Kb) [Save to disk]
  • Biological Unit Coordinates (5bs8.pdb1.gz) 816 Kb
  • LPC: Ligand-Protein Contacts for 5BS8
  • CSU: Contacts of Structural Units for 5BS8
  • Structure Factors (1424 Kb)
  • Retrieve 5BS8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BS8 from S2C, [Save to disk]
  • Re-refined 5bs8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5BS8 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 5BS8
  • 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
  • Fold representative 5bs8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5bs8_H] [5bs8_B] [5bs8_D] [5bs8] [5bs8_G] [5bs8_E] [5bs8_F] [5bs8_C] [5bs8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5BS8: [TOP2c] [TOP4c ] by SMART
  • Other resources with information on 5BS8
  • Community annotation for 5BS8 at PDBWiki (http://pdbwiki.org)

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