4RNG

Crystal structure of a bacterial homologue of SWEET transporters

• PDB DOI: https://doi.org/10.2210/pdb4RNG/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Thermodesulfovibrio yellowstonii DSM 11347
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2014-10-24 Released: 2014-11-19 
• Deposition Author(s): Hu, Q., Wang, J., Yan, C., Yan, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.251 

Literature

Crystal structure of a bacterial homologue of SWEET transporters.

Wang, J., Yan, C., Li, Y., Hirata, K., Yamamoto, M., Yan, N., Hu, Q.

(2014) Cell Res 24: 1486-1489

• PubMed: 25378180 
• DOI: https://doi.org/10.1038/cr.2014.144
• Primary Citation of Related Structures:  
  4RNG

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Organizational Affiliation: 

1] State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China [2] Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China [3] Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.24 kDa 
• Atom Count: 4,007 
• Modelled Residue Count: 494 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MtN3/saliva family	A, B, C, D, E, F	94	Thermodesulfovibrio yellowstonii DSM 11347	Mutation(s): 0  Gene Names: THEYE_A1538 Membrane Entity: Yes
UniProt
Find proteins for B5YGD6 (Thermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87)) Explore B5YGD6  Go to UniProtKB:  B5YGD6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	G [auth A], N [auth E], O [auth E], Q [auth F]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
SO4	H [auth A], I [auth A], J [auth B], K [auth C], L [auth D], M [auth D], P [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.251 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.88	α = 90
b = 96.155	β = 90
c = 119.797	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Hu, Q., Wang, J., Yan, C., Yan, N.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description