4BRR | pdb_00004brr

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 OPM PDBTM MemProtMD

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.252 (Depositor), 0.255 (DCC)
R-Value Work:
0.218 (Depositor), 0.223 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIACYLGLYCEROL KINASE	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABN1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
79M Query on 79M Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain L [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain L [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain L [auth D]	G [auth B], H [auth C], L [auth D]	(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate C₁₉ H₃₆ O₄ OWGMAJRKMYGYBQ-HJCTWCACSA-N		Interactions Focus chain G [auth B] Focus chain H [auth C] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth C] Focus chain L [auth D]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.252 (Depositor), 0.255 (DCC)
R-Value Work: 0.218 (Depositor), 0.223 (DCC)
R-Value Observed: 0.220 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-06-18

Deposition Author(s):

Li, D.

Howe, N.

Caffrey, M.

Revision History (Full details and data files)

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