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)

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
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Ligand Structure Quality Assessment

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Literature

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

Yang, B.B., Wang, N.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0C6B1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPD (Subject of Investigation/LOI) Query on SPD Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.