4BRR

Crystal structure of the integral membrane diacylglycerol kinase - delta 7.79

• PDB DOI: https://doi.org/10.2210/pdb4BRR/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2013-06-05 Released: 2014-06-18 
• Deposition Author(s): Li, D., Howe, N., Caffrey, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.252 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Starting Model: experimental

Literature

Crystal Structure of an Integral Membrane Enzyme Determined by X-Ray Free Electron Laser Femtocrystallography

Li, D., Howe, N., Caffrey, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.53 kDa 
• Atom Count: 4,563 
• Modelled Residue Count: 588 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIACYLGLYCEROL KINASE	A, B, C, D, E, F	130	Escherichia coli K-12	Mutation(s): 7  EC: 2.7.1.107 Membrane Entity: Yes
UniProt
Find proteins for P0ABN1 (Escherichia coli (strain K12)) Explore P0ABN1  Go to UniProtKB:  P0ABN1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
79M	G [auth B], H [auth C], L [auth D]	(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate C19 H36 O4 OWGMAJRKMYGYBQ-HJCTWCACSA-N
FLC	K [auth D]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
ZN	I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	J [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.252 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.06	α = 90
b = 91.5	β = 90
c = 143.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Li, D., Howe, N., Caffrey, M.

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Database references
• Version 1.2: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-04-03
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description