8ON5 | pdb_00008on5

Structure of the tail fibre from an extracellular contractile injection system from Photorhabdus bacteria

PDB DOI: https://doi.org/10.2210/pdb8ON5/pdb

Classification: CELL ADHESION
Organism(s): Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-31 Released: 2024-04-10
Deposition Author(s): Godfrey, A.E., Diaz-Saez, L.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.236 (Depositor), 0.240 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of the tail fibre from an extracellular contractile injection system from Photorhabdus bacteria

Godfrey, A.E., Diaz-Saez, L.

To be published.

Macromolecule Content

Total Structure Weight: 143.36 kDa
Atom Count: 9,980
Modeled Residue Count: 1,199
Deposited Residue Count: 1,302
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenoviral fiber protein	A, B, C, D, E A, B, C, D, E, F	217	Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949	Mutation(s): 0 Gene Names: PAU_02236
UniProt
Find proteins for C7BKQ5 (Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)) Explore C7BKQ5 Go to UniProtKB: C7BKQ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7BKQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain AA [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth F]	AA [auth F] G [auth A] I [auth A] L [auth B] N [auth B] AA [auth F], G [auth A], I [auth A], L [auth B], N [auth B], Q [auth C], S [auth C], T [auth D], W [auth E], Y [auth F], Z [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth F] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain V [auth E] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain V [auth E] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A]	H [auth A] J [auth A] M [auth B] O [auth B] P [auth C] H [auth A], J [auth A], M [auth B], O [auth B], P [auth C], R [auth C], U [auth D], V [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth E] Interactions & Density Focus chain H [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth E]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain K [auth B] MOL2 format, chain X [auth F] MOL2 format, chain K [auth B] mmCIF format, chain X [auth F] mmCIF format, chain K [auth B]	K [auth B], X [auth F]	UNKNOWN ATOM OR ION X		Interactions Focus chain K [auth B] Focus chain X [auth F] Interactions & Density Focus chain K [auth B] Focus chain X [auth F]