9IPT | pdb_00009ipt

Crystal structure of a TetR family regulator AmvR from Acinetobacter baumannii with spermidine bound

• PDB DOI: https://doi.org/10.2210/pdb9IPT/pdb

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


• Deposited: 2024-07-11 Released: 2025-07-16 
• 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: 2.50 Å
• R-Value Free: 
  0.270 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of a TetR family regulator AmvR from Acinetobacter baumannii with spermidine bound

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.58 kDa 
• Atom Count: 3,001 
• Modeled Residue Count: 372 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR family transcriptional regulator	A, B	192	Acinetobacter baumannii	Mutation(s): 0  Gene Names: ABCAM1_2317
UniProt
Find proteins for A0A7U3Y110 (Acinetobacter baumannii (strain ACICU)) Explore A0A7U3Y110  Go to UniProtKB:  A0A7U3Y110

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPD (Subject of Investigation/LOI)	C [auth A], D [auth B]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.270 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.005	α = 90
b = 65.51	β = 90
c = 101.032	γ = 90

Software Package:

Software Name	Purpose
autoPX	data processing
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
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: 2025-07-16
  Type: Initial release