9DGX | pdb_00009dgx

Monoclinic form of autolysin amidase AmiE

• PDB DOI: https://doi.org/10.2210/pdb9DGX/pdb

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


• Deposited: 2024-09-03 Released: 2026-03-18 
• Deposition Author(s): Loll, P.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Monoclinic form of autolysin amidase AmiE

Loll, P.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.94 kDa 
• Atom Count: 3,915 
• Modeled Residue Count: 414 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional autolysin	A, B	213	Staphylococcus epidermidis	Mutation(s): 0  Gene Names: atl, SERP0636 EC: 3.5.1.28 (PDB Primary Data), 3.2.1.96 (PDB Primary Data)
UniProt
Find proteins for Q5HQB9 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A)) Explore Q5HQB9  Go to UniProtKB:  Q5HQB9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.47	α = 90
b = 58.18	β = 95.3
c = 98.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PHENIX	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-18 
Deposition Author(s): Loll, P.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-03-18
  Type: Initial release