3LED | pdb_00003led

Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase III from Rhodopseudomonas palustris CGA009

• PDB DOI: https://doi.org/10.2210/pdb3LED/pdb

• Classification: TRANSFERASE
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-14 Released: 2010-01-26 
• Deposition Author(s): Chang, C., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.168 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase III from Rhodopseudomonas palustris CGA009

Chang, C., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A.

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.

Macromolecule Content 

• Total Structure Weight: 86.55 kDa 
• Atom Count: 7,400 
• Modeled Residue Count: 750 
• Deposited Residue Count: 784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-acyl carrier protein synthase III	A, B	392	Rhodopseudomonas palustris CGA009	Mutation(s): 0  Gene Names: RPA1298 EC: 2.3.1.41
UniProt
Find proteins for Q6NA87 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NA87  Go to UniProtKB:  Q6NA87

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth B], D [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.168 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.997	α = 90
b = 114.79	β = 96.8
c = 60.429	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Chang, C., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary