5IWI Isomerase date Mar 22, 2016
title 1.98a Structure Of Gsk945237 With S.Aureus Dna Gyrase And Si Nicked Dna
authors B.D.Bax, T.J.Miles
compound source
Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B
Chain: B, D
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes
 Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyrb, Sa0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Gyrase Subunit A
Chain: A, C
Ec: 5.99.1.3
Engineered: Yes
Organism_scientific: Staphylococcus Aureus (Strain N315)
Organism_taxid: 158879
Strain: N315
Gene: Gyra, Sa0006
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Apgpcpcpgptpapgpgptpapcpapcpcpgpcpapcp
Chain: E
Engineered: Yes
Other_details: Chain E Was A 20mer. Chain F Was An 8mer Tgt A 12mer Gtacctacggct. Note The 20mer, 8mer And 12mer Were A Together To Give A Nicked Dna Duplex. This Displayed Static Around The Non-Crystallographic Twofold Axis.;
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Tpgptpgpcpgpgptgptpapcpcptpapcpgpgpcp
Chain: F
Engineered: Yes
Other_details: Chain F Was An 8mer Tgtgcggt And A 12mer Gta . Could Be Described As Two Separate Chains. Note Chain E W 20mer. The 20mer, 8mer And 12mer Were Annealed Together To Nicked Dna Duplex. This Displayed Static Disorder Around Th Twofold Axis.;
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Tpgptpgpcpgpgptgptpapcpcptpapcpgpgpcp
Chain: G
Engineered: Yes
Other_details: Chain F Was An 8mer Tgtgcggt And A 12mer Gta . Could Be Described As Two Separate Chains. Note Chain E W 20mer. The 20mer, 8mer And 12mer Were Annealed Together To Nicked Dna Duplex. This Displayed Static Disorder Around Th Twofold Axis.
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 61
R_factor 0.166 R_Free 0.202
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.897 92.897 410.784 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.98 Å
ligand 6EJ, CL, GOL, MN enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (287 Kb) [Save to disk]
  • Biological Unit Coordinates (5iwi.pdb1.gz) 279 Kb
  • LPC: Ligand-Protein Contacts for 5IWI
  • CSU: Contacts of Structural Units for 5IWI
  • Structure Factors (2951 Kb)
  • Retrieve 5IWI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IWI from S2C, [Save to disk]
  • Re-refined 5iwi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5IWI 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 5IWI
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5iwi_A] [5iwi_E] [5iwi] [5iwi_C] [5iwi_B] [5iwi_G] [5iwi_F] [5iwi_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5IWI: [TOP2c] [TOP4c ] by SMART
    • Other resources with information on 5IWI
  • Community annotation for 5IWI at PDBWiki (http://pdbwiki.org)

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