3OCA | pdb_00003oca

Crystal structure of peptide deformylase from Ehrlichia chaffeensis

• PDB DOI: https://doi.org/10.2210/pdb3OCA/pdb

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


• Deposited: 2010-08-09 Released: 2010-09-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.246 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of peptide deformylase from Ehrlichia chaffeensis

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Sankaran, B., Edwards, T.E., Staker, B.

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: 47.97 kDa 
• Atom Count: 2,908 
• Modeled Residue Count: 358 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	209	Ehrlichia chaffeensis str. Arkansas	Mutation(s): 0  Gene Names: CDD:29602, def, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.246 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33OCA

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.26	α = 90
b = 64.43	β = 90
c = 80.91	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary