7X30 | pdb_00007x30

Capsid structure of Staphylococcus jumbo bacteriophage S6

PDB DOI: https://doi.org/10.2210/pdb7X30/pdb
EM Map EMD-32974: EMDB EMDataResource

Classification: VIRUS
Organism(s): Staphylococcus phage S6
Mutation(s): No

Deposited: 2022-02-27 Released: 2023-12-06
Deposition Author(s): Koibuchi, W., Uchiyama, J., Matsuzaki, S., Murata, K., Iwasaki, K., Miyazaki, N.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7X30

This is version 1.0 of the entry. See complete history.

Literature

Capsid structure of Staphylococcus jumbo bacteriophage S6

Koibuchi, W., Uchiyama, J., Matsuzaki, S., Murata, K., Iwasaki, K., Miyazaki, N.

To be published.

Macromolecule Content

Total Structure Weight: 1,812.6 kDa
Atom Count: 105,389
Modeled Residue Count: 13,432
Deposited Residue Count: 16,322
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major structural protein ORF12	A AA [auth z] B [auth a] C [auth b] D [auth c] A, AA [auth z], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e], G [auth f], H [auth g], I [auth h], J [auth i], K [auth j], L [auth k], M [auth l], N [auth m], O [auth n], P [auth o], Q [auth p], R [auth q], S [auth r], T [auth s], U [auth t], V [auth u], W [auth v], X [auth w], Y [auth x], Z [auth y]	534	Staphylococcus phage S6	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hoc-like protein ORF90	BA [auth P], CA [auth Q], DA [auth R], EA [auth S]	476	Staphylococcus phage S6	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15K18521
Japan Society for the Promotion of Science (JSPS)	Japan	18K06154

Revision History (Full details and data files)

Version 1.0: 2023-12-06
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.