5J46 | pdb_00005j46

Crystal structure of a Peptide Deformylase from Burkholderia multivorans

• PDB DOI: https://doi.org/10.2210/pdb5J46/pdb

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


• Deposited: 2016-03-31 Released: 2016-04-13 
• 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: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a Peptide Deformylase from Burkholderia multivorans

Potts, K.T., Abendroth, 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: 21.97 kDa 
• Atom Count: 1,414 
• Modeled Residue Count: 169 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	189	Burkholderia multivorans ATCC 17616	Mutation(s): 0  Gene Names: def, BMULJ_00106 EC: 3.5.1.88
UniProt
Find proteins for A0A0H3KB98 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KB98  Go to UniProtKB:  A0A0H3KB98

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35J46

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.72	α = 90
b = 69.07	β = 90
c = 119.87	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description