1W3M

Crystal structure of tsushimycin

PDB DOI: https://doi.org/10.2210/pdb1W3M/pdb

Classification: ANTIBIOTIC
Organism(s): Actinoplanes friuliensis
Mutation(s): No

Deposited: 2004-07-16 Released: 2005-07-27
Deposition Author(s): Bunkoczi, G., Vertesy, L., Sheldrick, G.M.

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

PubMed: 16041082 Search on PubMed
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

Macromolecule Content

Total Structure Weight: 18.23 kDa
Atom Count: 1,316
Modelled Residue Count: 132
Deposited Residue Count: 132
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TSUSHIMYCIN	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	11	Actinoplanes friuliensis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LNG Query on LNG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FB [auth I] SDF format, chain HA [auth D] SDF format, chain IB [auth J] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain OB [auth K] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain TA [auth G] SDF format, chain UB [auth L] SDF format, chain ZA [auth H] MOL2 format, chain AA [auth C] MOL2 format, chain FB [auth I] MOL2 format, chain HA [auth D] MOL2 format, chain IB [auth J] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain OB [auth K] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain UB [auth L] MOL2 format, chain ZA [auth H] mmCIF format, chain AA [auth C] mmCIF format, chain FB [auth I] mmCIF format, chain HA [auth D] mmCIF format, chain IB [auth J] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain OB [auth K] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain UB [auth L] mmCIF format, chain ZA [auth H]	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		Interactions Focus chain AA [auth C] Focus chain FB [auth I] Focus chain HA [auth D] Focus chain IB [auth J] Focus chain LA [auth E] Focus chain M [auth A] Focus chain OB [auth K] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain TA [auth G] Focus chain UB [auth L] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain FB [auth I] Focus chain HA [auth D] Focus chain IB [auth J] Focus chain LA [auth E] Focus chain M [auth A] Focus chain OB [auth K] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain TA [auth G] Focus chain UB [auth L] Focus chain ZA [auth H]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BA [auth C] SDF format, chain BB [auth H] SDF format, chain CB [auth H] SDF format, chain JB [auth J] SDF format, chain NB [auth J] SDF format, chain OA [auth E] SDF format, chain QB [auth K] SDF format, chain R [auth B] SDF format, chain UA [auth G] SDF format, chain VA [auth G] SDF format, chain X [auth B] SDF format, chain XB [auth L] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain PB [auth K] SDF format, chain S [auth B] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth H] MOL2 format, chain CB [auth H] MOL2 format, chain JB [auth J] MOL2 format, chain NB [auth J] MOL2 format, chain OA [auth E] MOL2 format, chain QB [auth K] MOL2 format, chain R [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] MOL2 format, chain X [auth B] MOL2 format, chain XB [auth L] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain PB [auth K] MOL2 format, chain S [auth B] mmCIF format, chain AB [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth H] mmCIF format, chain CB [auth H] mmCIF format, chain JB [auth J] mmCIF format, chain NB [auth J] mmCIF format, chain OA [auth E] mmCIF format, chain QB [auth K] mmCIF format, chain R [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain VA [auth G] mmCIF format, chain X [auth B] mmCIF format, chain XB [auth L] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain PB [auth K] mmCIF format, chain S [auth B]	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		Interactions Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CB [auth H] Focus chain JB [auth J] Focus chain NB [auth J] Focus chain OA [auth E] Focus chain PB [auth K] Focus chain QB [auth K] Focus chain R [auth B] Focus chain S [auth B] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain X [auth B] Focus chain XB [auth L] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CB [auth H] Focus chain JB [auth J] Focus chain NB [auth J] Focus chain OA [auth E] Focus chain PB [auth K] Focus chain QB [auth K] Focus chain R [auth B] Focus chain S [auth B] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain X [auth B] Focus chain XB [auth L] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain DB [auth H] SDF format, chain EA [auth C] SDF format, chain EB [auth H] SDF format, chain GB [auth I] SDF format, chain HB [auth I] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KB [auth J] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain RB [auth K] SDF format, chain SB [auth K] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain VB [auth L] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain YA [auth G] SDF format, chain CA [auth C] SDF format, chain LB [auth J] SDF format, chain MA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth H] MOL2 format, chain GB [auth I] MOL2 format, chain HB [auth I] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KB [auth J] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain RB [auth K] MOL2 format, chain SB [auth K] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth L] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain LB [auth J] MOL2 format, chain MA [auth E] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth H] mmCIF format, chain GB [auth I] mmCIF format, chain HB [auth I] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KB [auth J] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain RB [auth K] mmCIF format, chain SB [auth K] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain VB [auth L] mmCIF format, chain WA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain CA [auth C] mmCIF format, chain LB [auth J] mmCIF format, chain MA [auth E]	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		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain DB [auth H] Focus chain EA [auth C] Focus chain EB [auth H] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KB [auth J] Focus chain LB [auth J] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain RB [auth K] Focus chain SB [auth K] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VB [auth L] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain DB [auth H] Focus chain EA [auth C] Focus chain EB [auth H] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KB [auth J] Focus chain LB [auth J] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain RB [auth K] Focus chain SB [auth K] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VB [auth L] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain KA [auth D] SDF format, chain MB [auth J] SDF format, chain O [auth A] SDF format, chain SA [auth F] SDF format, chain TB [auth K] SDF format, chain W [auth B] SDF format, chain WB [auth L] SDF format, chain P [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain MB [auth J] MOL2 format, chain O [auth A] MOL2 format, chain SA [auth F] MOL2 format, chain TB [auth K] MOL2 format, chain W [auth B] MOL2 format, chain WB [auth L] MOL2 format, chain P [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain MB [auth J] mmCIF format, chain O [auth A] mmCIF format, chain SA [auth F] mmCIF format, chain TB [auth K] mmCIF format, chain W [auth B] mmCIF format, chain WB [auth L] mmCIF format, chain P [auth A]	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		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain KA [auth D] Focus chain MB [auth J] Focus chain O [auth A] Focus chain P [auth A] Focus chain SA [auth F] Focus chain TB [auth K] Focus chain W [auth B] Focus chain WB [auth L] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain KA [auth D] Focus chain MB [auth J] Focus chain O [auth A] Focus chain P [auth A] Focus chain SA [auth F] Focus chain TB [auth K] Focus chain W [auth B] Focus chain WB [auth L]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000487 Query on PRD_000487	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Tsushimycin	Lipopeptide / Antibiotic		Interactions Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

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 = 33.488	α = 65.64
b = 36.386	β = 68.35
c = 37.511	γ = 69.88

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling
SHELXD	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-07-27

Deposition Author(s):

Bunkoczi, G.

Vertesy, L.

Sheldrick, G.M.

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