8A42

Crystal structure of the pneumococcal Substrate-binding protein AmiA in complex with an unknown peptide

• PDB DOI: https://doi.org/10.2210/pdb8A42/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Streptococcus pneumoniae, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-06-10 Released: 2023-12-20 
• 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: 1.50 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 

Literature

Crystal structure of the pneumococcal Substrate-binding protein AmiA in complex with an unknown peptide

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.26 kDa 
• Atom Count: 5,671 
• Modelled Residue Count: 637 
• Deposited Residue Count: 648 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide-binding protein AmiA	A	638	Streptococcus pneumoniae	Mutation(s): 1  Gene Names: amiA, SP_1891
UniProt
Find proteins for P18791 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P18791  Go to UniProtKB:  P18791

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown peptide	B [auth G]	10	Escherichia coli	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.178 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.598	α = 90
b = 102.702	β = 90
c = 107.565	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
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: 2023-12-20
  Type: Initial release