4BRR

Crystal structure of the integral membrane diacylglycerol kinase - delta 7.79


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIACYLGLYCEROL KINASE
A, B, C, D, E, F
130Escherichia coli (strain K12)Mutation(s): 7 
Gene Names: dgkA
EC: 2.7.1.107
Find proteins for P0ABN1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABN1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FLC
Query on FLC

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Download CCD File 
D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
79M
Query on 79M

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Download CCD File 
B, C, D
(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate
[(2R)-2,3-bis(oxidanyl)propyl] (Z)-hexadec-7-enoate
C19 H36 O4
OWGMAJRKMYGYBQ-HJCTWCACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.060α = 90.00
b = 91.500β = 90.00
c = 143.720γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-04-03
    Type: Data collection, Experimental preparation