8XXA

Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains in complex with branched pentasaccharide

• PDB DOI: https://doi.org/10.2210/pdb8XXA/pdb

• Classification: HYDROLASE
• Organism(s): Rhodothermus marinus JCM 9785
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-18 Released: 2024-02-07 
• Deposition Author(s): Tonozuka, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.189 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

Structural basis for the recognition of alpha-1,6-branched alpha-glucan by GH13_47 alpha-amylase from Rhodothermus marinus

Miyasaka, Y., Yokoyama, K., Kozono, T., Kitano, Y., Miyazaki, T., Sakaguchi, M., Nishikawa, A., Tonozuka, T.

(2024) Proteins 

• DOI: https://doi.org/10.1002/prot.26695

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.51 kDa 
• Atom Count: 5,928 
• Modelled Residue Count: 620 
• Deposited Residue Count: 655 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-amylase	A	655	Rhodothermus marinus JCM 9785	Mutation(s): 0  EC: 3.2.1.1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D-glucopyranose-(1-4)]alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan:  G67645HZ GlyCosmos:  G67645HZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G96370VA GlyCosmos:  G96370VA GlyGen:  G96370VA

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009	C	alpha-maltotriose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.189 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.508	α = 90
b = 61.051	β = 106.11
c = 99.808	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Tonozuka, T.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20K05956

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2024-04-24
  Changes: Database references