4AL3

peptide deformylase (Co-form) with mercaptoethanol

• PDB DOI: https://doi.org/10.2210/pdb4AL3/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-29 Released: 2012-04-04 
• Deposition Author(s): Palm, G.J., Hinrichs, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.276 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

A Fret Enzyme-Based Probe for Monitoring Hydrogen Sulfide.

Strianese, M., Palm, G.J., Milione, S., Kuhl, O., Hinrichs, W., Pellecchia, C.

(2012) Inorg Chem 51: 11220

• PubMed: 23072298 
• DOI: https://doi.org/10.1021/ic301363d
• Primary Citation of Related Structures:  
  4AL2, 4AL3, 4AZ4


• PubMed Abstract: 
  

  Fluorescently labeled cobalt peptide deformylase (Co-PDF) can be efficiently used as a fluorescence-resonance-energy-transfer-based sensing device for hydrogen sulfide (H(2)S). The proof of concept of our sensor system is substantiated by spectroscopic, structural, and theoretical results. Monohydrogen sulfide coordination to Co-PDF and Ni-PDF was verified by X-ray crystallography. Density functional theory calculations were performed to gain insight into the characteristics of the coordination adduct between H(2)S and the cobalt cofactor in Co-PDF.

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Organizational Affiliation: 

Dipartimento di Chimica e Biologia, Università degli Studi di Salerno, via Ponte Don Melillo, I-84084 Fisciano (Sa), Italy. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 21.42 kDa 
• Atom Count: 1,415 
• Modelled Residue Count: 162 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE DEFORMYLASE	A	186	Escherichia coli BL21(DE3)	Mutation(s): 0  EC: 3.5.1.88
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12)) Explore P0A6K3  Go to UniProtKB:  P0A6K3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.276 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.63	α = 90
b = 55.63	β = 90
c = 229.34	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Palm, G.J., Hinrichs, W.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2012-06-06
  Changes: Other
• Version 1.2: 2012-10-31
  Changes: Database references
• Version 1.3: 2012-11-14
  Changes: Database references
• Version 1.4: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description