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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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. gabor.bunkoczi@sgc.ox.ac.uk


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
11Amorphoplanes 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
Biologically Interesting Molecules (External Reference) 1 Unique
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

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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