8XDX | pdb_00008xdx

Amylase A from Alkalimonas delamerensis

• PDB DOI: https://doi.org/10.2210/pdb8XDX/pdb

• Classification: HYDROLASE
• Organism(s): Alkalimonas delamerensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-11 Released: 2024-12-18 
• Deposition Author(s): Zhao, F., Xu, T.T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.180 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: in silico

Literature

Structure of amylase AmyA

Zhao, F., Xu, T.T.

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: 66.54 kDa 
• Atom Count: 4,441 
• Modeled Residue Count: 462 
• Deposited Residue Count: 587 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmyA	A	587	Alkalimonas delamerensis	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for A0A1H4DB11 (Alkalimonas amylolytica) Explore A0A1H4DB11  Go to UniProtKB:  A0A1H4DB11

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	B [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.180 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.469	α = 90
b = 71.433	β = 90
c = 146.535	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Zhao, F., Xu, T.T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release