9HVR | pdb_00009hvr

Native glucuronoyl esterase OtCE15A from Opitutus terrae

• PDB DOI: https://doi.org/10.2210/pdb9HVR/pdb

• Classification: HYDROLASE
• Organism(s): Opitutus terrae PB90-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-02 Released: 2026-01-14 
• Deposition Author(s): Oestberg, E.B., Lo Leggio, L., Zaghini, A., Mazurkewich, S., Larsbrink, J.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 

Starting Model: experimental

Literature

Interaction of a glucuronoyl esterase with complex fragments of the plant cell wall

Zaghini, A., Oestberg, E.B., Banerjee, S., Mazurkewich, S., Yu, L., Dupree, P., Larsbrink, J., Lo Leggio, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.15 kDa 
• Atom Count: 3,415 
• Modeled Residue Count: 393 
• Deposited Residue Count: 437 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acetyl xylan esterase	A	437	Opitutus terrae PB90-1	Mutation(s): 0  Gene Names: Oter_0116
UniProt
Find proteins for B1ZMF4 (Opitutus terrae (strain DSM 11246 / JCM 15787 / PB90-1)) Explore B1ZMF4  Go to UniProtKB:  B1ZMF4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.382	α = 90
b = 64.491	β = 90
c = 117.121	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-14 
Deposition Author(s): Oestberg, E.B., Lo Leggio, L., Zaghini, A., Mazurkewich, S., Larsbrink, J.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF21OC0071611

Revision History  

• Version 1.0: 2026-01-14
  Type: Initial release