8Z0C | pdb_00008z0c

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

• PDB DOI: https://doi.org/10.2210/pdb8Z0C/pdb

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


• Deposited: 2024-04-09 Released: 2025-04-16 
• Deposition Author(s): Yang, B.B., Wang, N.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.316 (Depositor), 0.322 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

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

Yang, B.B., 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

Macromolecule Content 

• Total Structure Weight: 43.08 kDa 
• Atom Count: 3,033 
• Modeled Residue Count: 372 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR family transcriptional regulator	A, B	186	Methylococcaceae	Mutation(s): 0  Gene Names: ABCAM1_2317, ABUW_1678, ACX61_07530, B9X95_03330, DOL94_11245, EA686_06095, F2P40_10030, FJV09_06005, GNY86_03815, HB367_07475
UniProt
Find proteins for D0C6B1 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0C6B1  Go to UniProtKB:  D0C6B1

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: 2.55 Å
• R-Value Free:  0.316 (Depositor), 0.322 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.84	α = 90
b = 65.52	β = 90
c = 100.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Yang, B.B., Wang, N.

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

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release