9ZMW | pdb_00009zmw

Crystal structure of a Iole protein from Brucella melitensis (orthorhombic P form 2)

• PDB DOI: https://doi.org/10.2210/pdb9ZMW/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Brucella melitensis bv. 1 str. 16M
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-12-11 Released: 2025-12-24 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of a Iole protein from Brucella melitensis (orthorhombic P form 2)

Liu, L., Lovell, S., Battaile, K.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 102.39 kDa 
• Atom Count: 7,149 
• Modeled Residue Count: 899 
• Deposited Residue Count: 921 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iole protein	A, B, C	307	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0  Gene Names: BMEII0570
UniProt
Find proteins for Q8YCG0 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YCG0  Go to UniProtKB:  Q8YCG0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.235 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.515	α = 90
b = 72.154	β = 90
c = 239.797	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release