6L3E | pdb_00006l3e

Crystal structure of Salmonella enterica sugar-binding protein MalE

• PDB DOI: https://doi.org/10.2210/pdb6L3E/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Salmonella enterica
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2019-10-10 Released: 2019-10-23 
• Deposition Author(s): Wang, L., Chen, Y., Liu, W., Lan, J., Shang, F., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

The crystal structure of Salmonella enterica sugar-binding protein MalE

Wang, L., Chen, Y., Liu, W., Lan, J., Shang, F., Xu, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 42.35 kDa 
• Atom Count: 3,383 
• Modeled Residue Count: 365 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein	A	370	Salmonella enterica	Mutation(s): 0  Gene Names: malE, AL463_06150, EDJ01_24875
UniProt
Find proteins for P19576 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P19576  Go to UniProtKB:  P19576

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G87171PZ GlyCosmos:  G87171PZ GlyGen:  G87171PZ

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC (Subject of Investigation/LOI)	K [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
TRS (Subject of Investigation/LOI)	L [auth A], M [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD (Subject of Investigation/LOI)	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL (Subject of Investigation/LOI)	N [auth A], O [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
2ME (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A]	METHOXYETHANE C3 H8 O XOBKSJJDNFUZPF-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	H [auth A], I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900010	B	alpha-maltotetraose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.714	α = 90
b = 89.692	β = 114.766
c = 64.066	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Wang, L., Chen, Y., Liu, W., Lan, J., Shang, F., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31200556
National Natural Science Foundation of China	China	21272031

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-03-27
  Changes: Data collection, Database references, Structure summary