9MRO | pdb_00009mro

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

PDB DOI: https://doi.org/10.2210/pdb9MRO/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: 1.59 Å
R-Value Free:
0.214 (Depositor), 0.214 (DCC)
R-Value Work:
0.209 (Depositor), 0.209 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 125.53 kDa
Atom Count: 10,132
Modeled Residue Count: 1,116
Deposited Residue Count: 1,140
Unique protein chains: 1

Macromolecules

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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	3D Interactions
ZDR (Subject of Investigation/LOI) Query on ZDR Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.214 (Depositor), 0.214 (DCC)
R-Value Work: 0.209 (Depositor), 0.209 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.622	α = 60.23
b = 103.771	β = 78.53
c = 103.77	γ = 78.54

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.