8XX9

Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains

• PDB DOI: https://doi.org/10.2210/pdb8XX9/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.175 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 

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: 76 kDa 
• Atom Count: 5,607 
• 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	D [auth A], E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
MPD	F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MN (Subject of Investigation/LOI)	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.175 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.77	α = 90
b = 102.389	β = 96.42
c = 63.397	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.

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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