6NOK | pdb_00006nok

The X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B1 protein loaded with myristic acid (C14:0) to 1.69 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6NOK/pdb

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


• Deposited: 2019-01-16 Released: 2019-08-21 
• Deposition Author(s): Cuypers, M.G., Gullett, J.M., 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: 1.69 Å
• R-Value Free: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

The X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B1 protein loaded with myristic acid (C14:0) to 1.69 Angstrom resolution

Cuypers, M.G., Gullett, J.M., 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)

Macromolecule Content 

• Total Structure Weight: 34.79 kDa 
• Atom Count: 2,587 
• Modeled Residue Count: 285 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty Acid Kinase (Fak) B1 protein	A	316	Streptococcus pneumoniae	Mutation(s): 0
UniProt
Find proteins for Q8DP17 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DP17  Go to UniProtKB:  Q8DP17

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYR (Subject of Investigation/LOI)	B [auth A]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36nok

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.556	α = 90
b = 66.324	β = 95.75
c = 46.953	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Cuypers, M.G., Gullett, J.M., 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: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description