5IDV | pdb_00005idv

Structure of the nucleotide binding domain of an ABC transporter MsbA from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb5IDV/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Acinetobacter baumannii AB5075
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-24 Released: 2016-03-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Structure of the nucleotide binding domain of an ABC transporter MsbA from Acinetobacter baumannii

Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.15 kDa 
• Atom Count: 2,438 
• Modeled Residue Count: 263 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid A export ATP-binding/permease protein MsbA	A	279	Acinetobacter baumannii AB5075	Mutation(s): 0  Gene Names: msbA, APC40_11520 EC: 3.6.3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35IDV

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.22	α = 90
b = 89.03	β = 90
c = 104.14	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
Coot	model building
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description