7L4L | pdb_00007l4l

Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C8-crypto Acyl Carrier Protein, AcpP

• PDB DOI: https://doi.org/10.2210/pdb7L4L/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-19 Released: 2021-09-22 
• Deposition Author(s): Mindrebo, J.T., Chen, A., Kim, W.E., Burkart, M.D., Noel, J.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Structure and Mechanistic Analyses of the Gating Mechanism of Elongating Ketosynthases

Mindrebo, J.T., Chen, A., Kim, W.E., Re, R.N., Davis, T.D., Noel, J.P., Burkart, M.D.

(2021) ACS Catal 11: 6787-6799

• DOI: https://doi.org/10.1021/acscatal.1c00745

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 104.45 kDa 
• Atom Count: 7,265 
• Modeled Residue Count: 973 
• Deposited Residue Count: 982 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 2	A, B	413	Escherichia coli K-12	Mutation(s): 0  Gene Names: fabF, fabJ, b1095, JW1081 EC: 2.3.1.179
UniProt
Find proteins for P0AAI5 (Escherichia coli (strain K12)) Explore P0AAI5  Go to UniProtKB:  P0AAI5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	C, D	78	Escherichia coli K-12	Mutation(s): 0  Gene Names: acpP, b1094, JW1080
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8  Go to UniProtKB:  P0A6A8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DYF (Subject of Investigation/LOI)	G [auth C], H [auth D]	[(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate C19 H36 N3 O8 P KFHBREMVHHVYJE-IJDCCNJMSA-N
NA	E [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.782	α = 90
b = 92.136	β = 90
c = 113.746	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-22 
Deposition Author(s): Mindrebo, J.T., Chen, A., Kim, W.E., Burkart, M.D., Noel, J.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	095970-09

Revision History  

• Version 1.0: 2021-09-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary