6AQZ | pdb_00006aqz

Crystal structure of a gdp-l-fucose synthetase from Naegleria fowleri bound to NADP

• PDB DOI: https://doi.org/10.2210/pdb6AQZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Naegleria fowleri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-21 Released: 2017-08-30 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.224 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a gdp-l-fucose synthetase from Naegleria fowleri bound to NADP

Edwards, T.E., Dranow, D.M., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 237.94 kDa 
• Atom Count: 15,349 
• Modeled Residue Count: 1,949 
• Deposited Residue Count: 2,046 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gdp-l-fucose synthetase	A, B, C, D, E, F	341	Naegleria fowleri	Mutation(s): 0  EC: 1.1.1.271
UniProt
Find proteins for A0A2D0TCK0 (Naegleria fowleri) Explore A0A2D0TCK0  Go to UniProtKB:  A0A2D0TCK0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	G [auth A], H [auth B], J [auth C], K [auth E], L [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
EDO	I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.224 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36AQZ

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.37	α = 90
b = 104.03	β = 108.67
c = 120.17	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Data collection
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary
• Version 1.5: 2025-10-22
  Changes: Database references, Structure summary