6PYK | pdb_00006pyk

P. mirabilis hemolysin A mutant - F80L

• PDB DOI: https://doi.org/10.2210/pdb6PYK/pdb

• Classification: TOXIN
• Organism(s): Proteus mirabilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-07-30 Released: 2020-08-05 
• Deposition Author(s): Weaver, T.M., Novak, W.R.P., Bhattacharyya, B.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

Structure of truncated hemolysin A variant F80L

Weaver, T.M., Novak, W.R.P., Bhattacharyya, B., Woods, C.N., Grilley, D.P., Wimmer, M.R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 25.45 kDa 
• Atom Count: 1,962 
• Modeled Residue Count: 241 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin	A	242	Proteus mirabilis	Mutation(s): 1  Gene Names: hpmA
UniProt
Find proteins for P16466 (Proteus mirabilis) Explore P16466  Go to UniProtKB:  P16466

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.55	α = 90
b = 34.011	β = 101.02
c = 59.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Weaver, T.M., Novak, W.R.P., Bhattacharyya, B.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB1050435
National Science Foundation (NSF, United States)	United States	REU1434473

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary