4JGA | pdb_00004jga

X-ray crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase 2 from Rickettsia rickettsii

• PDB DOI: https://doi.org/10.2210/pdb4JGA/pdb

• Classification: TRANSFERASE
• Organism(s): Rickettsia rickettsii str. 'Sheila Smith
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-28 Released: 2013-05-29 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase 2 from Rickettsia rickettsii

Fairman, J.W., Abendroth, J.A., Edwards, T.E., Lorimer, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.52 kDa 
• Atom Count: 6,830 
• Modeled Residue Count: 844 
• Deposited Residue Count: 874 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 2	A, B	437	Rickettsia rickettsii str. 'Sheila Smith	Mutation(s): 0  Gene Names: A1G_06510 EC: 2.3.1.179
UniProt
Find proteins for A0A0H3AY56 (Rickettsia rickettsii (strain Sheila Smith)) Explore A0A0H3AY56  Go to UniProtKB:  A0A0H3AY56

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	C [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34JGA

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.17	α = 90
b = 62.74	β = 112.08
c = 95.43	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description