3U04 | pdb_00003u04

Crystal structure of peptide deformylase from ehrlichia chaffeensis in complex with actinonin

• PDB DOI: https://doi.org/10.2210/pdb3U04/pdb

• Classification: HYDROLASE/HYDROLASE INHIBTIOR
• Organism(s): Ehrlichia chaffeensis str. Arkansas
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-28 Released: 2011-10-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.198 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of peptide deformylase from ehrlichia chaffeensis in complex with actinonin

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Clifton, M.C., Edwards, T.E., Staker, B.L.

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: 22.26 kDa 
• Atom Count: 1,563 
• Modeled Residue Count: 172 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase 1	A	190	Ehrlichia chaffeensis str. Arkansas	Mutation(s): 0  Gene Names: def, def1, ECH_0073 EC: 3.5.1.88
UniProt
Find proteins for Q2GI30 (Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas)) Explore Q2GI30  Go to UniProtKB:  Q2GI30

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	E [auth A]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.198 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33U04

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.89	α = 90
b = 33.02	β = 91.17
c = 68.14	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description