8QLC

Crystal structure of the pneumococcal Substrate-binding protein AliD in open conformation

• PDB DOI: https://doi.org/10.2210/pdb8QLC/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-19 Released: 2024-05-22 
• Deposition Author(s): Alcorlo, M., Abdullah, M.R., Hammerschmidt, S., Hermoso, J.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

Crystal structure of the pneumococcal Substrate-binding protein AliD in open conformation

Alcorlo, M., Abdullah, M.R., Hammerschmidt, S., Hermoso, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.26 kDa 
• Atom Count: 5,515 
• Modelled Residue Count: 624 
• Deposited Residue Count: 627 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AliD	A	627	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: aliD
UniProt
Find proteins for H2BJN6 (Streptococcus pneumoniae) Explore H2BJN6  Go to UniProtKB:  H2BJN6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.241	α = 90
b = 93.003	β = 90
c = 111.648	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Alcorlo, M., Abdullah, M.R., Hammerschmidt, S., Hermoso, J.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2020-115331GB-I00

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release