6IYG | pdb_00006iyg

The Structure of Maltooligosaccharide-forming Amylase from Pseudomonas saccharophila STB07 with Maltotetraose

• PDB DOI: https://doi.org/10.2210/pdb6IYG/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Roseateles saccharophilus
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2018-12-15 Released: 2019-12-18 
• Deposition Author(s): Li, Z.F., Ban, X.F., Zhang, Z.Q., Li, C.M., Gu, Z.B., Jin, T.C., Li, Y.L., Shang, Y.H.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.186 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Maltotetraose-forming amylase from Pseudomonas saccharophila STB07

Zhang, Z.Q., Ban, X.F., Li, Z.F., Jin, T.C., Li, Y.L., Gu, Z.B., Li, C.M., Shang, Y.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.43 kDa 
• Atom Count: 3,679 
• Modeled Residue Count: 415 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucan 1,4-alpha-maltotetraohydrolase	A	536	Roseateles saccharophilus	Mutation(s): 0  Gene Names: mta EC: 3.2.1.60
UniProt
Find proteins for P22963 (Roseateles saccharophilus) Explore P22963  Go to UniProtKB:  P22963

Oligosaccharides

Help  

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	B	4		N/A
Glycosylation Resources
GlyTouCan: G87171PZ GlyCosmos: G87171PZ GlyGen: G87171PZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900010	B	alpha-maltotetraose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.186 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.28	α = 90
b = 64.57	β = 90
c = 168.91	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Li, Z.F., Ban, X.F., Zhang, Z.Q., Li, C.M., Gu, Z.B., Jin, T.C., Li, Y.L., Shang, Y.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31722040
National Natural Science Foundation of China	China	31571882

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary