4F8N

X-ray structure of PsaA from Yersinia pestis, in complex with galactose and phosphate choline

• PDB DOI: https://doi.org/10.2210/pdb4F8N/pdb

• Classification: CELL ADHESION
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-17 Released: 2013-05-22 
• Deposition Author(s): Bao, R., Esser, L., Xia, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.282 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.71 kDa 
• Atom Count: 1,187 
• Modelled Residue Count: 137 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pH 6 antigen	A	145	Yersinia pestis	Mutation(s): 0  Gene Names: psaA, y2882, YPO1303, YP_1289
UniProt
Find proteins for P31522 (Yersinia pestis) Explore P31522  Go to UniProtKB:  P31522

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PC	C [auth A]	PHOSPHOCHOLINE C5 H15 N O4 P YHHSONZFOIEMCP-UHFFFAOYSA-O
GAL	E [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
GAI	B [auth A]	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
GAL	Binding MOAD:  4F8N	IC50: 4.00e+7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.282 
• R-Value Work: 0.245 
• R-Value Observed: 0.247 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.154	α = 90
b = 54.922	β = 90
c = 103.271	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Bao, R., Esser, L., Xia, D.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-08-07
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-28
  Changes: Data collection, Database references, Structure summary