6XV5 | pdb_00006xv5

Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with ertapenem

• PDB DOI: https://doi.org/10.2210/pdb6XV5/pdb

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


• Deposited: 2020-01-21 Released: 2021-02-03 
• Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.285 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 

Starting Model: experimental

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: native gel electrophoresis

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 132.17 kDa 
• Atom Count: 8,700 
• Modeled Residue Count: 1,069 
• 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 BBB], B [auth AAA]	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
TLA	C [auth AAA]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
O2E	A [auth BBB], B [auth AAA]	L-PEPTIDE LINKING	C25 H32 N4 O9 S		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.285 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.265	α = 90
b = 147.772	β = 90
c = 164.523	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description