5NDX | pdb_00005ndx

The bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I

• PDB DOI: https://doi.org/10.2210/pdb5NDX/pdb

• Classification: HYDROLASE
• Organism(s): Rhizobium leguminosarum bv. trifolii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-09 Released: 2018-07-11 
• Deposition Author(s): Raich, L., Valero-Gonzalez, J., Castro-Lopez, J., Millan, C., Jimenez-Garcia, M.J., Nieto, P., Uson, I., Hurtado-Guerrero, R., Rovira, C.
• Funding Organization(s): MICINN

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.175 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: other

Literature

The bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I.

Raich, L., Valero-Gonzalez, J., Castro-Lopez, J., Millan, C., Jimenez-Garcia, M.J., Nieto, P., Uson, I., Hurtado-Guerrero, R., Rovira, C.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.64 kDa 
• Atom Count: 5,235 
• Modeled Residue Count: 606 
• Deposited Residue Count: 621 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase	A	621	Rhizobium leguminosarum bv. trifolii	Mutation(s): 2  Gene Names: BAE36_24485
UniProt
Find proteins for A0A1B8R7L2 (Rhizobium leguminosarum bv. trifolii) Explore A0A1B8R7L2  Go to UniProtKB:  A0A1B8R7L2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8U8	M [auth A], N [auth A]	(2~{R},3~{S},4~{S},5~{R},6~{S})-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid C16 H16 O9 ARQXEQLMMNGFDU-ZHMBSYLPSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.175 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.028	α = 90
b = 173.028	β = 90
c = 156.687	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-07-11 
Deposition Author(s): Raich, L., Valero-Gonzalez, J., Castro-Lopez, J., Millan, C., Jimenez-Garcia, M.J., Nieto, P., Uson, I., Hurtado-Guerrero, R., Rovira, C.

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Funding Organization	Location	Grant Number
MICINN	Spain	CTQ2013-44367-C2-2-P
MICINN	Spain	BFU2016-75633-P
MICINN	Spain	CTQ2014-55174

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary