5NGY | pdb_00005ngy

Crystal structure of Leuconostoc citreum NRRL B-1299 dextransucrase DSR-M

• PDB DOI: https://doi.org/10.2210/pdb5NGY/pdb

• Classification: TRANSFERASE
• Organism(s): Leuconostoc citreum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-20 Released: 2017-11-01 
• Deposition Author(s): Claverie, M., Cioci, G., Remaud-simeon, M., Moulis, C., Tranier, S., Vuillemin, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Investigations on the Determinants Responsible for Low Molar Mass Dextran Formation by DSR-M Dextransucrase

Claverie, M., Cioci, G., Vuillemin, M., Monties, N., Roblin, P., Lippens, G., Remaud-simeon, M., Moulis, C.

(2017) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.7b02182

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 289.55 kDa 
• Atom Count: 18,858 
• Modeled Residue Count: 2,409 
• Deposited Residue Count: 2,580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DSR-M glucansucrase inactive mutant E715Q	A, B	1,290	Leuconostoc citreum	Mutation(s): 0  EC: 2.4.1.5
UniProt
Find proteins for A0A2H4A2Q1 (Leuconostoc citreum) Explore A0A2H4A2Q1  Go to UniProtKB:  A0A2H4A2Q1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose	C	4		N/A
Glycosylation Resources
GlyTouCan:  G80662SX GlyCosmos:  G80662SX GlyGen:  G80662SX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PR	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N
CA	D [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.869	α = 90
b = 128.81	β = 90
c = 234.518	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Claverie, M., Cioci, G., Remaud-simeon, M., Moulis, C., Tranier, S., Vuillemin, M.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary