7KMX | pdb_00007kmx

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

Validation slider image for 7KMX

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
Modeled Residue Count: 3,178
Deposited Residue Count: 3,388
Unique protein chains: 2

Macromolecules

Find similar proteins by:

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

Find similar proteins by:

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

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

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View more in-depth experimental data

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

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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.