5T8Z | pdb_00005t8z

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

• PDB DOI: https://doi.org/10.2210/pdb5T8Z/pdb

• Classification: hydrolase/antibiotic
• Organism(s): Burkholderia multivorans ATCC 17616
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-08 Released: 2016-10-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• 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: 1.85 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

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

Irwin, R.M., Abendroth, J., Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

To be published.

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: 21.36 kDa 
• Atom Count: 1,401 
• Modeled Residue Count: 161 
• Deposited Residue Count: 185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	185	Burkholderia multivorans ATCC 17616	Mutation(s): 0  Gene Names: def, BMULJ_01994 EC: 3.5.1.88
UniProt
Find proteins for A0A0H3KPJ9 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KPJ9  Go to UniProtKB:  A0A0H3KPJ9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	B [auth A]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35T8Z

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.12	α = 90
b = 70.54	β = 90
c = 140.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
Coot	model building
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description