7YXV | pdb_00007yxv

Crystal structure of a tautomerase superfamily member form Acinetobacter baumanii

• PDB DOI: https://doi.org/10.2210/pdb7YXV/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-16 Released: 2022-05-18 
• Deposition Author(s): Pankov, G., Hunter, W.N.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

The structure of a tautomerase superfamily member linked to the type VI secretion system of Acinetobacter baumannii.

Pankov, G., Mol Avelar, G., Buchanan, G., Coulthurst, S.J., Hunter, W.N.

(2023) Acta Crystallogr F Struct Biol Commun 79: 8-16

• PubMed: 36598351 
• DOI: https://doi.org/10.1107/S2053230X22011414
• Primary Citation of Related Structures:  
  7YXV


• PubMed Abstract: 
  

  Bacteria exploit specialized secretion systems to assist in competition for resources, in collaboration and in communication. Here, a protocol for the recombinant production, purification and crystallization of a protein linked to the Acinetobacter baumannii type VI secretion system is provided. A high-resolution structure of this trimeric protein is reported, revealing the characteristic dual β-α-β subunit fold typical of longer subunit members of the tautomerase superfamily. The protein does not appear to be toxic to bacteria or yeast under the conditions tested. The possible biological role of this protein is discussed.

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Organizational Affiliation: 
• Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.41 kDa 
• Atom Count: 1,200 
• Modeled Residue Count: 121 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate synthase	A	129	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  A7M90_11190, AB945B12_02656, Aba9201_05520, ABR2091_1504, ABUW_2349, ACX61_10775, APC21_13445, C6N18_08520, CBE85_12580, E1A86_09085, E1A87_16805, EA686_20000, EA706_14840, EGM95_12490, F2P40_09685, FGL68_10230, FJU36_18545, FR761_08425, G3N53_00085, GNY86_01620, GSE42_08590, GUK62_04465, H0529_06935, HB367_04115, NCTC13421_02212, SAMEA104305385_02323, SI89_13245
UniProt
Find proteins for A0A077GKT8 (Acinetobacter baumannii) Explore A0A077GKT8  Go to UniProtKB:  A0A077GKT8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.185	α = 90
b = 59.185	β = 90
c = 97.757	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): Pankov, G., Hunter, W.N.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	215599/Z/19/Z

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release
  
• Version 1.1: 2023-01-25
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description