6TUD | pdb_00006tud

Crystal structure of Y. pestis penicillin-binding protein 3

• PDB DOI: https://doi.org/10.2210/pdb6TUD/pdb

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


• Deposited: 2020-01-06 Released: 2021-01-27 
• Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.250 (DCC) 

Starting Model: experimental

Literature

The structure of penicillin-binding protein 3 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: 119.12 kDa 
• Atom Count: 7,046 
• Modeled Residue Count: 928 
• Deposited Residue Count: 1,098 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase FtsI	A [auth AAA], B [auth BBB]	549	Yersinia pestis	Mutation(s): 0  Gene Names: ftsI, YPO0549 EC: 3.4.16.4
UniProt
Find proteins for A0A3N4B5A3 (Yersinia pestis) Explore A0A3N4B5A3  Go to UniProtKB:  A0A3N4B5A3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.250 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.8	α = 90
b = 100.8	β = 90
c = 314.409	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description