6C84 | pdb_00006c84

Crystal structure of PBP5 from Enterococcus faecium

• PDB DOI: https://doi.org/10.2210/pdb6C84/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Enterococcus faecium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-24 Released: 2019-02-06 
• Deposition Author(s): Shamoo, Y., Davlieva, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Crystal structure of PBP5 from Enterococcus faecium

Shamoo, Y., Davlieva, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 143.71 kDa 
• Atom Count: 9,797 
• Modeled Residue Count: 1,281 
• Deposited Residue Count: 1,318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein	A, B	659	Enterococcus faecium	Mutation(s): 0  Gene Names: CQR40_00950, HMPREF3199_01318

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.977	α = 90
b = 73.071	β = 114.97
c = 131.445	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Shamoo, Y., Davlieva, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R22430

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2022-03-23
  Changes: Author supporting evidence, Database references
• Version 1.3: 2024-05-22
  Changes: Data collection