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: https://doi.org/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 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. [email protected]


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TSUSHIMYCIN
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
11Actinoplanes friuliensisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LNG
Query on LNG
Download Ideal Coordinates CCD File 
AA [auth C]
FB [auth I]
HA [auth D]
IB [auth J]
LA [auth E]
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
EOH
Query on EOH
Download Ideal Coordinates CCD File 
AB [auth H]
BA [auth C]
BB [auth H]
CB [auth H]
JB [auth J]
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
CA
Query on CA
Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
DB [auth H]
EA [auth C]
EB [auth H]
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
CL
Query on CL
Download Ideal Coordinates CCD File 
FA [auth C]
GA [auth C]
KA [auth D]
MB [auth J]
O [auth A]
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
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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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