7KMX

The capsid of Myoviridae Phage XM1

PDB DOI: https://doi.org/10.2210/pdb7KMX/pdb
EM Map EMD-22931: EMDB EMDataResource

Classification: VIRUS
Organism(s): Vibrio phage XM1
Mutation(s): No

Deposited: 2020-11-03 Released: 2021-11-10
Deposition Author(s): Wang, Z., Klose, T., Jiang, W., Kuhn, R.J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Vibrio phage XM1, a simple contractile DNA injection machine

Wang, Z., Fokine, A., Guo, X., Jiang, W., Rossmann, M.G., Kuhn, R.J., Luo, Z.H., Klose, T.

(2021) bioRxiv

DOI: https://doi.org/10.1101/2021.12.18.469577

Macromolecule Content

Total Structure Weight: 366.36 kDa
Atom Count: 24,045
Modelled Residue Count: 3,178
Deposited Residue Count: 3,388
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor capsid protein	A [auth a] B [auth b] C [auth c] D [auth d] E [auth e] A [auth a], B [auth b], C [auth c], D [auth d], E [auth e], F [auth f], G [auth g]	160	Vibrio phage XM1	Mutation(s): 0
UniProt
Find proteins for A0A7D7FKF5 (Vibrio phage XM1) Explore A0A7D7FKF5 Go to UniProtKB: A0A7D7FKF5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7D7FKF5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	H [auth A] I [auth B] J [auth C] K [auth D] L [auth E] H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G]	324	Vibrio phage XM1	Mutation(s): 0
UniProt
Find proteins for A0A7D7J3A3 (Vibrio phage XM1) Explore A0A7D7J3A3 Go to UniProtKB: A0A7D7J3A3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7D7J3A3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	jspr

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-11-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-11-10
Type: Initial release
Version 1.1: 2022-05-25
Changes: Database references, Derived calculations
Version 1.2: 2024-05-29
Changes: Data collection, Database references

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 R01GM133198.