8G1L

Lectin domain of Aap (Staphylococcus epidermidis Accumulation Associated Protein)

• PDB DOI: https://doi.org/10.2210/pdb8G1L/pdb

• Classification: CELL ADHESION
• Organism(s): Staphylococcus epidermidis RP62A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-02 Released: 2024-02-14 
• Deposition Author(s): Maciag, J.J., Herr, A.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.126 
• R-Value Work: 0.117 
• R-Value Observed: 0.117 

Literature

Mechanistic basis of staphylococcal interspecies competition for skin colonization

Maciag, J.J., Herr, A.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS, assay for oligomerization

Macromolecule Content

• Total Structure Weight: 27.72 kDa 
• Atom Count: 2,369 
• Modelled Residue Count: 252 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Accumulation associated protein	A	252	Staphylococcus epidermidis RP62A	Mutation(s): 0  Gene Names: aap, SERP2398
UniProt
Find proteins for Q5HKE8 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A)) Explore Q5HKE8  Go to UniProtKB:  Q5HKE8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG0	H [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.126 
• R-Value Work: 0.117 
• R-Value Observed: 0.117 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.664	α = 90
b = 68.573	β = 90
c = 109.272	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
pointless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Maciag, J.J., Herr, A.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM094363
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI162964

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release