7XAQ

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)

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7W2O 7W2Q

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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] 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HZP1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

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

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-26

Deposition Author(s):

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

Revision History (Full details and data files)

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

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.