5V85

The crystal structure of the protein of DegV family COG1307 from Ruminococcus gnavus ATCC 29149 (alternative refinement of PDB 3JR7 with Vaccenic acid)

• PDB DOI: https://doi.org/10.2210/pdb5V85/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mediterraneibacter gnavus ATCC 29149
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-03-21 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: 2.00 Å
• R-Value Free: 0.198 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3JR7

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 Biol Chem 

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)

Macromolecule Content

• Total Structure Weight: 68.26 kDa 
• Atom Count: 5,055 
• Modelled Residue Count: 557 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EDD domain protein, DegV family	A, B	298	Mediterraneibacter gnavus ATCC 29149	Mutation(s): 0  Gene Names: RUMGNA_03254
UniProt
Find proteins for A7B6P0 (Mediterraneibacter gnavus (strain ATCC 29149 / DSM 114966 / JCM 6515 / VPI C7-9)) Explore A7B6P0  Go to UniProtKB:  A7B6P0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VCA	C [auth A], H [auth B]	VACCENIC ACID C18 H34 O2 UWHZIFQPPBDJPM-FPLPWBNLSA-N
PO4	D [auth A], E [auth A], F [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	G [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.198 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.899	α = 90
b = 96.899	β = 90
c = 159.921	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	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: 2024-10-16
  Changes: Data collection, Database references, Structure summary