4WER | pdb_00004wer

Crystal structure of diacylglycerol kinase catalytic domain protein from Enterococcus faecalis V583

• PDB DOI: https://doi.org/10.2210/pdb4WER/pdb

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


• Deposited: 2014-09-10 Released: 2014-09-24 
• Deposition Author(s): Chang, C., Clancy, S., Hatzos-Skintges, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Crystal structure of diacylglycerol kinase catalytic domain protein from Enterococcus faecalis V583

Chang, C., Clancy, S., Hatzos-Skintges, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content 

• Total Structure Weight: 33.67 kDa 
• Atom Count: 2,420 
• Modeled Residue Count: 285 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diacylglycerol kinase catalytic domain protein	A	303	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF_2644, I574_02965, OO5_00903
UniProt
Find proteins for Q830X4 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q830X4  Go to UniProtKB:  Q830X4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.05 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.271	α = 90
b = 103.157	β = 90
c = 44.478	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Chang, C., Clancy, S., Hatzos-Skintges, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary