4CK0 | pdb_00004ck0

Crystal structure of the integral membrane diacylglycerol kinase - form 2

• PDB DOI: https://doi.org/10.2210/pdb4CK0/pdb

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


• Deposited: 2013-12-23 Released: 2015-01-28 
• Deposition Author(s): Li, D., Lyons, J.A., Vogeley, L., Aragao, D., Caffrey, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Integral Membrane Diacylglycerol Kinase with Zn-Amppcp Bound and its Catalytic Mechanism

Li, D., 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)

Macromolecule Content 

• Total Structure Weight: 44.07 kDa 
• Atom Count: 2,647 
• Modeled Residue Count: 332 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIACYLGLYCEROL KINASE	A, B, C	130	Escherichia coli K-12	Mutation(s): 4  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP	H [auth C]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
OLC	D [auth B], E [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
ZN	F [auth C], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.82	α = 90
b = 72.82	β = 90
c = 195.67	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Li, D., Lyons, J.A., Vogeley, L., Aragao, D., Caffrey, M.

Revision History  

• Version 1.0: 2015-01-28
  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: 2023-03-29
  Changes: Database references, Derived calculations, Other, Structure summary
• Version 1.5: 2024-02-07
  Changes: Data collection, Refinement description