5VCP

Crystal structure of a peptide deformylase from Burkholderia xenovorans in complex with actinonin

• PDB DOI: https://doi.org/10.2210/pdb5VCP/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-31 Released: 2017-05-03 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.192 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Crystal structure of a peptide deformylase from Burkholderia xenovorans in complex with actinonin

Conrady, D.G., Abendroth, J., Lorimer, D.D., Edwards, T.E.

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 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: 85.61 kDa 
• Atom Count: 5,417 
• Modelled Residue Count: 640 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B, C, D	185	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: def, Bxe_A1677 EC: 3.5.1.88
UniProt
Find proteins for Q13XB1 (Paraburkholderia xenovorans (strain LB400)) Explore Q13XB1  Go to UniProtKB:  Q13XB1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	F [auth A], I [auth B], M [auth C], O [auth D]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
FE2	E [auth A], H [auth B], L [auth C], N [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
MG	G [auth A], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.192 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M35VCP

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.11	α = 90
b = 90.33	β = 90
c = 140.21	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description