6CK7

Crystal structure of a peptide deformylase from Legionella pneumophila bound to actinonin

• PDB DOI: https://doi.org/10.2210/pdb6CK7/pdb

• Classification: HYDROLASE/ANTIBIOTIC
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-27 Released: 2018-03-07 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.208 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

Crystal structure of a peptide deformylase from Legionella pneumophila bound to actinonin

Edwards, T.E., Horanyi, P.S., Lorimer, D.D.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83.44 kDa 
• Atom Count: 6,262 
• Modelled Residue Count: 688 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B, C, D	178	Legionella pneumophila	Mutation(s): 0  Gene Names: def_2, def, def_1, def_3, A1D14_13265, A9P85_13750, ERS240541_01674, ERS240560_02189, ERS253249_00325, lpymg_02824 EC: 3.5.1.88
UniProt
Find proteins for Q5ZSC4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSC4  Go to UniProtKB:  Q5ZSC4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	F [auth A], I [auth B], L [auth C], P [auth D]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
SO4	G [auth A], J [auth B], M [auth C], N [auth C], Q [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], H [auth B], K [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.208 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M36CK7

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.65	α = 90
b = 132.06	β = 103.64
c = 90.38	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description