8DU0 | pdb_00008du0

Crystal Structure of NADP bound GDP-L-fucose synthase from Brucella ovis

• PDB DOI: https://doi.org/10.2210/pdb8DU0/pdb

• Classification: ISOMERASE
• Organism(s): Brucella ovis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-26 Released: 2022-08-10 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: in silico

Literature

Crystal Structure of NADP bound GDP-L-fucose synthase from Brucella ovis

DeBouver, N.D., Davies, D.R., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.73 kDa 
• Atom Count: 2,233 
• Modeled Residue Count: 286 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-L-fucose synthase	A	334	Brucella ovis	Mutation(s): 0  Gene Names: fcl, BOV_A0361 EC: 1.1.1.271
UniProt
Find proteins for A0A0H3AU93 (Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512)) Explore A0A0H3AU93  Go to UniProtKB:  A0A0H3AU93

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.82	α = 90
b = 75.82	β = 90
c = 112.53	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
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
Not funded		--

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2024-02-14
  Changes: Data collection
• Version 1.2: 2024-04-03
  Changes: Refinement description