8FI6 | pdb_00008fi6

Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase) (NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA (Orthorhombic P Form 3)

• PDB DOI: https://doi.org/10.2210/pdb8FI6/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania major strain Friedlin
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-12-15 Released: 2022-12-28 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.211 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase) (NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA (Orthorhombic P Form 3)

Lovell, S., Battaile, K.P., Staker, B.L., Liu, L.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.15 kDa 
• Atom Count: 3,639 
• Modeled Residue Count: 411 
• Deposited Residue Count: 425 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A	425	Leishmania major strain Friedlin	Mutation(s): 1  Gene Names: LMJFC_320006100 EC: 2.3.1.97
UniProt
Find proteins for Q4Q5S8 (Leishmania major) Explore Q4Q5S8  Go to UniProtKB:  Q4Q5S8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA (Subject of Investigation/LOI)	B [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.211 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38FI6

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.809	α = 90
b = 88.62	β = 90
c = 92.49	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	OD030394

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection