9PI2 | pdb_00009pi2

X-ray crystal structure of Ancylobacter lacus LanM bound to Nd(III) and Ca(II)

PDB DOI: https://doi.org/10.2210/pdb9PI2/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Ancylobacter lacus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-10 Released: 2026-08-19
Deposition Author(s): Jung, J.J., Boal, A.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.99 Å
R-Value Free:
0.144 (Depositor), 0.138 (DCC)
R-Value Work:
0.136 (Depositor), 0.130 (DCC)
R-Value Observed:
0.136 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Near-Adjacent Heavy Lanthanide Separation and Sensing Using Dimerizing Lanmodulins

Choi, W., Zhou, X., Dong, Z., Song, F., Jung, J.J., Mattocks, J.A., Chlebek, J.L., Diep, P., Johnson, A.C., Crawford, S.E., Jiao, Y., Honaker, R., Boal, A.K., Park, D.M., Cotruvo, J.A.J.

(2026) J Am Chem Soc 148: 36817-36831

DOI: https://doi.org/10.1021/jacs.6c08525

Macromolecule Content

Total Structure Weight: 25.69 kDa
Atom Count: 2,189
Modeled Residue Count: 222
Deposited Residue Count: 222
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancylobacter lacus lanthanum bound protein	A, B	111	Ancylobacter lacus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ND (Subject of Investigation/LOI) Query on ND Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] H [auth B] I [auth B] C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	Neodymium Ion Nd UYIXUPGBIXNDHN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]