7M5H

Crystal structure of conserved protein from Enterococcus faecalis V583

• PDB DOI: https://doi.org/10.2210/pdb7M5H/pdb
• Entry: 7M5H supersedes: 3EHD

• Classification: TRANSFERASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-23 Released: 2021-04-07 
• Deposition Author(s): Nocek, B., Wu, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.217 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Crystal structure of conserved protein from Enterococcus faecalis V583

Nocek, B., Wu, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.32 kDa 
• Atom Count: 2,741 
• Modelled Residue Count: 317 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside 2-deoxyribosyltransferase	A, B	162	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF_2354
UniProt
Find proteins for Q831Y8 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q831Y8  Go to UniProtKB:  Q831Y8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], E [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.15 Å
• R-Value Free: 0.217 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 219.901	α = 90
b = 219.901	β = 90
c = 219.901	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
SHELXD	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Nocek, B., Wu, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 3EHD

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary