6TIX | pdb_00006tix

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

• PDB DOI: https://doi.org/10.2210/pdb6TIX/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

The structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam

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: 131.76 kDa 
• Atom Count: 8,270 
• Modeled Residue Count: 1,031 
• 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
DH4	C [auth AAA], D [auth BBB]	2-[(1R)-1-{[(E)-azepan-1-ylmethylidene]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C15 H25 N3 O3 S GIESTXBEHWEDNC-XRSRENSCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.240 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.172	α = 112.917
b = 84.035	β = 95.306
c = 87.099	γ = 104.566

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	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
• Version 1.2: 2024-10-23
  Changes: Structure summary