2XCR Isomerase date Apr 25, 2010
title The 3.5a Crystal Structure Of The Catalytic Core (B'A' Region) Of Staphylococcus Aureus Dna Gyrase Complexed With Gsk299423 And Dna
authors B.D.Bax, P.F.Chan, D.S.Eggleston, A.Fosberry, D.R.Gentry, F.Gorre I.Giordano, M.M.Hann, A.Hennessy, M.Hibbs, J.Huang, E.Jones, J.Jo K.K.Brown, C.J.Lewis, E.W.May, O.Singh, C.Spitzfaden, C.Shen, A.S A.F.Theobald, A.Wohlkonig, N.D.Pearson, M.N.Gwynn
compound source
Molecule: Dna Gyrase Subunit B, Dna Gyrase Subunit A
Chain: B, D, S, U
Fragment: C-Terminal 27kda Domain, Residues 410-644, N-Term 56kda Domain, Residues 2-491;
Engineered: Yes
Mutation: Yes
Other_details: C-Terminus Gyrb (B644) Fused To N-Terminus G
Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: 5'-D(5uagpcpcpgptpapgpgpgpcpcpcptp Gpcptp)-3';
Chain: E, F

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Apgpcpcpgptpapgpgpgpcpcpcptpa Gpcptp)-3';
Chain: V, W

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.2082 R_Free 0.2582
length a length b length c angle alpha angle beta angle gamma
113.260 165.381 308.431 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand 5UA, RXV enzyme Isomerase E.C. BRENDA
S, D, B, U

Primary referenceType IIA topoisomerase inhibition by a new class of antibacterial agents., Bax BD, Chan PF, Eggleston DS, Fosberry A, Gentry DR, Gorrec F, Giordano I, Hann MM, Hennessy A, Hibbs M, Huang J, Jones E, Jones J, Brown KK, Lewis CJ, May EW, Saunders MR, Singh O, Spitzfaden CE, Shen C, Shillings A, Theobald AF, Wohlkonig A, Pearson ND, Gwynn MN, Nature. 2010 Aug 4. PMID:20686482
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1065 Kb) [Save to disk]
  • Biological Unit Coordinates (2xcr.pdb1.gz) 531 Kb
  • Biological Unit Coordinates (2xcr.pdb2.gz) 530 Kb
  • LPC: Ligand-Protein Contacts for 2XCR
  • CSU: Contacts of Structural Units for 2XCR
  • Structure Factors (524 Kb)
  • Retrieve 2XCR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XCR from S2C, [Save to disk]
  • Re-refined 2xcr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XCR 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 2XCR
  • 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
  • 3D motif for 2XCR, from MSDmotif at EBI
  • Fold representative 2xcr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xcr_W] [2xcr] [2xcr_F] [2xcr_U] [2xcr_V] [2xcr_S] [2xcr_B] [2xcr_D] [2xcr_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XCR: [TOP2c] [TOP4c ] by SMART
  • Other resources with information on 2XCR
  • Community annotation for 2XCR at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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