9MRP | pdb_00009mrp

Crystal structures of a cyanobacterial DAP epimerase bound to L,L-aziDAP

• PDB DOI: https://doi.org/10.2210/pdb9MRP/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: in silico

Literature

Crystal structures of a cyanobacterial DAP epimerase bound to L,L-aziDAP

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: 9,555 
• 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
UniProt
Find proteins for A0A5Q0GFR1 (Anabaena sp. YBS01) Explore A0A5Q0GFR1  Go to UniProtKB:  A0A5Q0GFR1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.46	α = 90
b = 102.596	β = 103.13
c = 47.674	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	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.

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

Revision History  

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