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)

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
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This is version 1.0 of the entry. See complete history.

Literature

Structure of amylase AmyA

Zhao, F., Xu, T.T.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1H4DB11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-12-18
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.