7XAQ | pdb_00007xaq

Cryo-EM structure of PvrA-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb7XAQ/pdb
• NAKB: 7XAQ
• EM Map EMD-33097: EMDB EMDataResource

• Classification: TRANSCRIPTION
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: synthetic construct, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2022-03-18 Released: 2023-04-26 
• Deposition Author(s): Zhu, Y.B., Su, Z.M., Bao, R.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

The Pseudomonas aeruginosa regulator PvrA binds cooperatively to multiple pseudo-palindromic sites to efficiently stimulate target gene

Zhu, Y.B., Luo, B.N., Song, Y.J., Su, Z.M., Bao, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 203.39 kDa 
• Atom Count: 13,396 
• Modeled Residue Count: 1,369 
• Deposited Residue Count: 1,444 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulator	E [auth B], F [auth A], G, H [auth C], I [auth H], J [auth D]	212	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA2957
UniProt
Find proteins for Q9HZP1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HZP1  Go to UniProtKB:  Q9HZP1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
fadD1	A [auth F], C [auth E]	43	Pseudomonas aeruginosa PAO1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
fadD1	B [auth J], D [auth I]	43	Pseudomonas aeruginosa PAO1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.1
MODEL REFINEMENT	PHENIX	1.15
MODEL REFINEMENT	Coot	0.8

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Zhu, Y.B., Su, Z.M., Bao, R.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81871615

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2023-07-26
  Changes: Other
• Version 1.2: 2024-06-26
  Changes: Data collection, Refinement description
• Version 1.3: 2025-03-12
  Changes: Data collection, Database references, Structure summary