1W3M

Crystal structure of tsushimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.171 
  • R-Value Observed: 0.137 

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This is version 1.4 of the entry. See complete history


Literature

Structure of the lipopeptide antibiotic tsushimycin.

Bunkoczi, G.Vertesy, L.Sheldrick, G.M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1160-1164

  • DOI: 10.1107/S0907444905017270
  • Primary Citation of Related Structures:  
    1W3M

  • PubMed Abstract: 
  • The amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 A resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods ...

    The amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 A resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods. The antibiotic is comprised of a cyclodecapeptide core, an exocyclic amino acid and a fatty-acid residue. Its backbone adopts a saddle-like conformation that is stabilized by a Ca2+ ion bound within the peptide ring and accounts for the Ca2+-dependence of this antibiotic class. Additional Ca2+ ions link the antibiotic molecules to dimers that enclose an empty space resembling a binding cleft. The dimers possess a large hydrophobic surface capable of interacting with the bacterial cell membrane. The antibiotic daptomycin may exhibit a similar conformation, as the amino-acid sequence is conserved at positions involved in Ca2+ binding.


    Organizational Affiliation

    Lehrstuhl für Strukturchemie, Georg-August Universität, Tammannstrasse 4, 37077 Göttingen, Germany. gabor.bunkoczi@sgc.ox.ac.uk



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TSUSHIMYCIN
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
11Actinoplanes friuliensisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LNG (Subject of Investigation/LOI)
Query on LNG

Download Ideal Coordinates CCD File 
AA [auth C] , FB [auth I] , HA [auth D] , IB [auth J] , LA [auth E] , M [auth A] , OB [auth K] , PA [auth F] , 
AA [auth C],  FB [auth I],  HA [auth D],  IB [auth J],  LA [auth E],  M [auth A],  OB [auth K],  PA [auth F],  Q [auth B],  TA [auth G],  UB [auth L],  ZA [auth H]
Delta-3isotetradecenoic acid
C14 H26 O2
CPJZLQGGCFWOAA-NTMALXAHSA-N
 Ligand Interaction
EOH
Query on EOH

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AB [auth H] , BA [auth C] , BB [auth H] , CB [auth H] , JB [auth J] , NB [auth J] , OA [auth E] , PB [auth K] , 
AB [auth H],  BA [auth C],  BB [auth H],  CB [auth H],  JB [auth J],  NB [auth J],  OA [auth E],  PB [auth K],  QB [auth K],  R [auth B],  S [auth B],  UA [auth G],  VA [auth G],  X [auth B],  XB [auth L],  Y [auth B],  Z [auth B]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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CA [auth C] , DA [auth C] , DB [auth H] , EA [auth C] , EB [auth H] , GB [auth I] , HB [auth I] , IA [auth D] , 
CA [auth C],  DA [auth C],  DB [auth H],  EA [auth C],  EB [auth H],  GB [auth I],  HB [auth I],  IA [auth D],  JA [auth D],  KB [auth J],  LB [auth J],  MA [auth E],  N [auth A],  NA [auth E],  QA [auth F],  RA [auth F],  RB [auth K],  SB [auth K],  T [auth B],  U [auth B],  V [auth B],  VB [auth L],  WA [auth G],  XA [auth G],  YA [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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FA [auth C] , GA [auth C] , KA [auth D] , MB [auth J] , O [auth A] , P [auth A] , SA [auth F] , TB [auth K] , 
FA [auth C],  GA [auth C],  KA [auth D],  MB [auth J],  O [auth A],  P [auth A],  SA [auth F],  TB [auth K],  W [auth B],  WB [auth L]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000487
Query on PRD_000487
A, B, C, D, E, F, G, H, I, J, K, LTsushimycinLipopeptide /  Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.171 
  • R-Value Observed: 0.137 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.488α = 65.64
b = 36.386β = 68.35
c = 37.511γ = 69.88
Software Package:
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Changes: Other
  • Version 1.3: 2018-10-31
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Refinement description
  • Version 1.4: 2019-05-22
    Changes: Data collection, Derived calculations, Refinement description