6TII

Crystal structure of penicillin-binding protein 2 from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb6TII/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-22 Released: 2020-12-02 
• Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.253 
• R-Value Work: 0.191 

Literature

The structure of penicillin-binding protein 2 from Yersinia pestis

Pankov, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 131.27 kDa 
• Atom Count: 8,753 
• Modelled Residue Count: 1,068 
• Deposited Residue Count: 1,166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase MrdA	A [auth AAA], B [auth BBB]	583	Yersinia pestis	Mutation(s): 0  Gene Names: mrdA, YPO2604 EC: 3.4.16.4
UniProt
Find proteins for A0A0H2W2Y2 (Yersinia pestis) Explore A0A0H2W2Y2  Go to UniProtKB:  A0A0H2W2Y2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	C [auth AAA], D [auth BBB]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.253 
• R-Value Work: 0.191 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.661	α = 113.467
b = 84.773	β = 94.972
c = 88.359	γ = 103.725

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description