9C8Y

X-ray crystal structure of Methylorubrum extorquens Ce(III)-bound LanD

• PDB DOI: https://doi.org/10.2210/pdb9C8Y/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Methylorubrum extorquens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-13 Released: 2024-10-16 
• Deposition Author(s): Jung, J.J., Lin, C.-Y., Boal, A.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

Modulating metal-centered dimerization of a lanthanide chaperone protein for separation of light lanthanides

Larrinaga, W.B., Jung, J.J., Lin, C.-Y., Boal, A.K., Cotruvo, J.A.

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)

Macromolecule Content

• Total Structure Weight: 6.74 kDa 
• Atom Count: 498 
• Modelled Residue Count: 60 
• Deposited Residue Count: 61 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
landiscernin	A	61	Methylorubrum extorquens	Mutation(s): 0  Gene Names: LanD
UniProt
Find proteins for C5B159 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5B159  Go to UniProtKB:  C5B159

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CE (Subject of Investigation/LOI)	B [auth A]	CERIUM (III) ION Ce XQTIWNLDFPPCIU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.086	α = 90
b = 78.086	β = 90
c = 78.086	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Jung, J.J., Lin, C.-Y., Boal, A.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release