5X6E

Crystal structure of PrfA-DNA binary complex

PDB DOI: https://doi.org/10.2210/pdb5X6E/pdb
NAKB: 5X6E

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-21 Released: 2017-04-12
Deposition Author(s): Wang, Y., Feng, H., Zhu, Y.L., Gao, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.300
R-Value Work: 0.249
R-Value Observed: 0.252

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into glutathione-mediated activation of the master regulator PrfA in Listeria monocytogenes

Wang, Y., Feng, H., Zhu, Y., Gao, P.

(2017) Protein Cell 8: 308-312

PubMed: 28271443 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s13238-017-0390-x
Primary Citation of Related Structures:
5X6D, 5X6E

Organizational Affiliation

Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 219.3 kDa
Atom Count: 15,154
Modelled Residue Count: 1,588
Deposited Residue Count: 1,596
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Listeriolysin positive regulatory factor A	A [auth M] B [auth N] E [auth A] F [auth B] I [auth E] A [auth M], B [auth N], E [auth A], F [auth B], I [auth E], J [auth F]	237	Listeria monocytogenes	Mutation(s): 0 Gene Names: prfA, AJL40_05990, AJN46_04535, M643_11230
UniProt
Find proteins for P22262 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore P22262 Go to UniProtKB: P22262
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22262
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (29-MER)	C [auth O], G [auth C], K [auth G]	29	Listeria monocytogenes
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	D [auth P], H [auth D], L [auth H]	29	Listeria monocytogenes
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download Ideal Coordinates CCD File SDF format, chain M SDF format, chain N SDF format, chain O [auth A] SDF format, chain Q [auth E] SDF format, chain P [auth B] SDF format, chain R [auth F] MOL2 format, chain M MOL2 format, chain N MOL2 format, chain O [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth B] MOL2 format, chain R [auth F]	M N O [auth A] P [auth B] Q [auth E] M, N, O [auth A], P [auth B], Q [auth E], R [auth F]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain M Focus chain N Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth E] Focus chain R [auth F] Interactions & Density Focus chain M Focus chain N Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth E] Focus chain R [auth F]