7AG5 | pdb_00007ag5

Structure of the Laspartomycin C double mutant G4D D-allo-Thr9D-Dap in complex with Geranyl phosphate

• PDB DOI: https://doi.org/10.2210/pdb7AG5/pdb

• Classification: ANTIBIOTIC
• Organism(s): Streptomyces viridochromogenes
• Mutation(s): No 


• Deposited: 2020-09-21 Released: 2022-02-02 
• Deposition Author(s): Zeronian, M.R., Pearce, N.M., Wood, T.M., Martin, N.I., Janssen, B.J.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 
  0.143 (Depositor), 0.145 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.123 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Starting Model: experimental

Literature

Mechanistic insights into the C55-P targeting lipopeptide antibiotics revealed by structure-activity studies and high-resolution crystal structures

Wood, T.M., Zeronian, M.R., Buijs, N., Bertheussen, K., Abedian, H.K., Johnson, A.V., Pearce, N.M., Lutz, M., Kemmink, J., Seirsma, T., Hamoen, L.W., Janssen, B.J.C., Martin, N.I.

(2022) Chem Sci 13: 2985-2991

• DOI: https://doi.org/10.1039/D1SC07190D

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 1.64 kDa 
• Atom Count: 158 
• Modeled Residue Count: 11 
• Deposited Residue Count: 11 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laspartomycin C double mutant G4D D-allo-Thr9D-Dap	A	11	Streptomyces viridochromogenes	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9GE	E [auth A]	(~{E})-13-methyltetradec-2-enoic acid C15 H28 O2 HNGBGNIRFVZXOQ-ACCUITESSA-N
RDZ	D [auth A]	Geranyl phosphate C10 H19 O4 P FFOWJDCTFSWUMJ-JXMROGBWSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2RA	A	D-PEPTIDE LINKING	C3 H8 N2 O2		ALA
CPI	A	D-PEPTIDE LINKING	C6 H11 N O2		--
DNP	A	L-PEPTIDE LINKING	C3 H9 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free:  0.143 (Depositor), 0.145 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.123 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.428	α = 90
b = 40.428	β = 90
c = 31.033	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Aimless	data scaling
STARANISO	data scaling
DIALS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Zeronian, M.R., Pearce, N.M., Wood, T.M., Martin, N.I., Janssen, B.J.C.

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2022-03-23
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description