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

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
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wwPDB Validation 3D Report Full Report

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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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O66934
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
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 Query on PRD_900030	E, F, G, H	alpha-maltopentaose	Oligosaccharide / Substrate analog		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.