5UXY | pdb_00005uxy

The crystal structure of a DegV family protein from Eubacterium eligens loaded with heptadecanoic acid to 1.80 Angstrom resolution (ALTERNATIVE REFINEMENT OF PDB 3FDJ with HEPTADECANOIC acid)

• PDB DOI: https://doi.org/10.2210/pdb5UXY/pdb

• Classification: TRANSFERASE
• Organism(s): Lachnospira eligens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-23 Released: 2018-11-21 
• Deposition Author(s): Cuypers, M.G., Ericson, M., subramanian, C., White, S.W., Rock, C.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3FDJ

Literature

The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein loaded with palmitic acid to 1.83 Angstroem resolution

Cuypers, M.G., Ericson, M., Subramanian, C., Broussard, T.C., Miller, D.J., White, S.W., Rock, C.O.

(2018) J Biological Chem 

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: 31.09 kDa 
• Atom Count: 2,557 
• Modeled Residue Count: 276 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DegV family protein	A	278	Lachnospira eligens	Mutation(s): 0
UniProt
Find proteins for D0VX07 (Lachnospira eligens) Explore D0VX07  Go to UniProtKB:  D0VX07

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X90	D [auth A]	heptadecanoic acid C17 H34 O2 KEMQGTRYUADPNZ-UHFFFAOYSA-N
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.445	α = 90
b = 57.445	β = 90
c = 186.558	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Cuypers, M.G., Ericson, M., subramanian, C., White, S.W., Rock, C.O.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary