5I2B | pdb_00005i2b

Crystal structure of a peptide deformylase from Burkholderia ambifaria with actinonin

• PDB DOI: https://doi.org/10.2210/pdb5I2B/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia ambifaria IOP40-10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-08 Released: 2016-03-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.204 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a peptide deformylase from Burkholderia ambifaria with actinonin

Conrady, D.G., Dranow, D.M., 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)

Macromolecule Content 

• Total Structure Weight: 21.66 kDa 
• Atom Count: 1,507 
• Modeled Residue Count: 167 
• Deposited Residue Count: 185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	185	Burkholderia ambifaria IOP40-10	Mutation(s): 0  Gene Names: def, BamIOP4010DRAFT_5965 EC: 3.5.1.88
UniProt
Find proteins for B1FPK4 (Burkholderia ambifaria IOP40-10) Explore B1FPK4  Go to UniProtKB:  B1FPK4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	C [auth A]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.204 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35I2B

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.59	α = 90
b = 70.25	β = 90
c = 140.73	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description