9IYZ | pdb_00009iyz

Crystal Structure of the Acinetobacter baumannii LysR family regulator AceR DNA-binding domain (P321)

• PDB DOI: https://doi.org/10.2210/pdb9IYZ/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Acinetobacter baumannii ATCC 17978
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-31 Released: 2025-08-06 
• Deposition Author(s): Ma, J.M., Ge, H.H., Wang, N.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: in silico

Literature

Crystal Structure of the Acinetobacter baumannii LysR family regulator AceR DNA-binding domain (P321)

Ma, J.M., Ge, H.H., Wang, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.21 kDa 
• Atom Count: 2,049 
• Modeled Residue Count: 250 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator AceR	A, B, C	90	Acinetobacter baumannii ATCC 17978	Mutation(s): 0  Gene Names: aceR, A1S_2064
UniProt
Find proteins for P0DUU5 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore P0DUU5  Go to UniProtKB:  P0DUU5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.14	α = 90
b = 87.14	β = 90
c = 73.362	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Ma, J.M., Ge, H.H., Wang, N.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071215

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release