9OLP | pdb_00009olp

Crystal structure of a raffinose-bound D59C MelB

• PDB DOI: https://doi.org/10.2210/pdb9OLP/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. 101966
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-05-12 Released: 2026-02-04 
• Deposition Author(s): Guan, L., Hariharan, P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.329 (Depositor), 0.329 (DCC) 
• R-Value Work: 
  0.316 (Depositor), 0.316 (DCC) 
• R-Value Observed: 
  0.317 (Depositor) 

Starting Model: experimental

Literature

Allosteric effects of the coupling cation in melibiose transporter MelB

Hariharan, P., Shi, Y., Amirhossein, B., Liang, R., Viner, R., Guan, L.

(2026) Elife 

• DOI: https://doi.org/10.7554/elife.108335.2

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.6 kDa 
• Atom Count: 3,581 
• Modeled Residue Count: 453 
• Deposited Residue Count: 485 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Melibiose permease	A	485	Salmonella enterica subsp. enterica serovar Typhimurium str. 101966	Mutation(s): 1  Gene Names: melB, STM4299
UniProt
Find proteins for P30878 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P30878  Go to UniProtKB:  P30878

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose	B	3		N/A

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900002	B	raffinose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.329 (Depositor), 0.329 (DCC) 
• R-Value Work:  0.316 (Depositor), 0.316 (DCC) 
• R-Value Observed: 0.317 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.103	α = 90
b = 127.103	β = 90
c = 104.882	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Guan, L., Hariharan, P.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM153222

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release