9JLR | pdb_00009jlr

Crystal structure of GH57 family amylopullulanase from Aquifex aeolicus mutant E256Q in complex with maltopentaose

• PDB DOI: https://doi.org/10.2210/pdb9JLR/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-09-19 Released: 2025-06-04 
• Deposition Author(s): Zhu, Z.M., Wang, W.W., Li, M.J., Xu, Q., Zhou, H., Huang, L.Q., Wang, Q.S., Yu, F.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.245 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: in silico

Literature

High-Temperature Crystallization Method for the GH57 Family Hyperthermophilic Amylopullulanase from Aquifex aeolicus

Zhu, Z., Wang, W., Huang, L., Xu, Q., Zhou, H., Li, M., Yu, F., Wang, Q.

(2024) Cryst Growth Des 24: 10350-10357

• DOI: https://doi.org/10.1021/acs.cgd.4c01306

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 236.61 kDa 
• Atom Count: 16,627 
• Modeled Residue Count: 1,923 
• Deposited Residue Count: 1,940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 57 N-terminal domain-containing protein	A, B, C, D	485	Aquifex aeolicus VF5	Mutation(s): 1  Gene Names: aq_720
UniProt
Find proteins for O66934 (Aquifex aeolicus (strain VF5)) Explore O66934  Go to UniProtKB:  O66934

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-(1-4)-alpha-D-glucopyranose	E, F, G, H	5		N/A
Glycosylation Resources
GlyTouCan:  G50146AM GlyCosmos:  G50146AM

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900030	E, F, G, H	alpha-maltopentaose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.245 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.17	α = 90
b = 165.17	β = 109.46
c = 98.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Zhu, Z.M., Wang, W.W., Li, M.J., Xu, Q., Zhou, H., Huang, L.Q., Wang, Q.S., Yu, F.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release