9MRV | pdb_00009mrv

Crystal structures of a cyanobacterial DAP epimerase bound to D,L-alpha-methyl DAP

• PDB DOI: https://doi.org/10.2210/pdb9MRV/pdb

• Classification: ANTIBIOTIC
• Organism(s): Anabaena sp. YBS01
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-08 Released: 2025-07-16 
• Deposition Author(s): Chen, P., Lamer, T., Vederas, J.C., Lemieux, M.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: in silico

Literature

Crystal structures of a cyanobacterial DAP epimerase bound to diaminopimelic acid analogues

Lamer, T., Chen, P., Lemieux, M.J., Vederas, J.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 125.53 kDa 
• Atom Count: 10,247 
• Modeled Residue Count: 1,116 
• Deposited Residue Count: 1,140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate epimerase	A, B, C, D	285	Anabaena sp. YBS01	Mutation(s): 0  Gene Names: dapF, EH233_12580 EC: 5.1.1.7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZDR (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID C8 H16 N2 O4 TVZGBXIJPFGQBJ-YLWLKBPMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.496	α = 61.01
b = 103.878	β = 78.42
c = 103.865	γ = 78.62

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Chen, P., Lamer, T., Vederas, J.C., Lemieux, M.J.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release