8WK0 | pdb_00008wk0

Cryo-EM structure of a bacterial protein

PDB DOI: https://doi.org/10.2210/pdb8WK0/pdb
EM Map EMD-37592: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Paenibacillus sp. 453mf
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-26 Released: 2024-09-11
Deposition Author(s): Yu, G., Liao, F., Li, X., Li, Z., Zhang, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.34 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8WK0

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

Literature

Cryo-EM structure of a bacterial protein

Yu, G., Liao, F., Li, X., Li, Z., Zhang, H.

To be published.

Macromolecule Content

Total Structure Weight: 468.5 kDa
Atom Count: 26,968
Modeled Residue Count: 3,486
Deposited Residue Count: 4,176
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase HerA central domain-containing protein	A B [auth D] C [auth M] D [auth N] E [auth O] A, B [auth D], C [auth M], D [auth N], E [auth O], F [auth L]	696	Paenibacillus sp. 453mf	Mutation(s): 0 Gene Names: SAMN04488601_104156

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain O [auth L] SDF format, chain M [auth O] SDF format, chain K [auth N] SDF format, chain I [auth M] SDF format, chain G [auth D] MOL2 format, chain O [auth L] MOL2 format, chain M [auth O] MOL2 format, chain K [auth N] MOL2 format, chain I [auth M] MOL2 format, chain G [auth D] mmCIF format, chain O [auth L] mmCIF format, chain M [auth O] mmCIF format, chain K [auth N] mmCIF format, chain I [auth M] mmCIF format, chain G [auth D]	G [auth D], I [auth M], K [auth N], M [auth O], O [auth L]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain G [auth D] Focus chain I [auth M] Focus chain K [auth N] Focus chain M [auth O] Focus chain O [auth L] Interactions & Density Focus chain G [auth D] Focus chain I [auth M] Focus chain K [auth N] Focus chain M [auth O] Focus chain O [auth L]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth L] SDF format, chain N [auth O] SDF format, chain L [auth N] SDF format, chain J [auth M] SDF format, chain H [auth D] MOL2 format, chain P [auth L] MOL2 format, chain N [auth O] MOL2 format, chain L [auth N] MOL2 format, chain J [auth M] MOL2 format, chain H [auth D] mmCIF format, chain P [auth L] mmCIF format, chain N [auth O] mmCIF format, chain L [auth N] mmCIF format, chain J [auth M] mmCIF format, chain H [auth D]	H [auth D], J [auth M], L [auth N], N [auth O], P [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth D] Focus chain J [auth M] Focus chain L [auth N] Focus chain N [auth O] Focus chain P [auth L] Interactions & Density Focus chain H [auth D] Focus chain J [auth M] Focus chain L [auth N] Focus chain N [auth O] Focus chain P [auth L]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.34 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32200496

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release
Version 1.1: 2025-07-02
Changes: Data collection, Structure summary

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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.