6DJ6 | pdb_00006dj6

The X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B2 protein loaded with cis-oleic acid to 1.9 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6DJ6/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-24 Released: 2019-05-29 
• Deposition Author(s): Cuypers, M.G., Subramanian, C., White, S.W., Rock, C.O.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: in silico

Literature

The X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B2 protein (SPR1019) loaded with cis-oleic acid to 1.9 Angstrom resolution

Cuypers, M.G., Subramanian, C., White, S.W., Rock, C.O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.7 kDa 
• Atom Count: 5,028 
• Modeled Residue Count: 555 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty Acid Kinase (Fak) B2 protein (SPR1019)	A, B	313	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: SPR1019

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLA	G [auth A], J [auth B]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.227 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.72	α = 90
b = 103.851	β = 90
c = 108.174	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Cuypers, M.G., Subramanian, C., White, S.W., Rock, C.O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2024-03-13
  Changes: Advisory, Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description