8XUA | pdb_00008xua

Outer membrane protein from Vibrio campbellii 25 kDa (OmpV25)

PDB DOI: https://doi.org/10.2210/pdb8XUA/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio harveyi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2024-01-12 Released: 2024-12-25
Deposition Author(s): Meesrikaew, P., Sanram, S., Robinson, R., Suginta, W.
Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.268 (Depositor), 0.269 (DCC)
R-Value Work:
0.209 (Depositor), 0.211 (DCC)
R-Value Observed:
0.212 (Depositor)

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

Ligand Structure Quality Assessment

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

Literature

Outer membrane protein from Vibrio campbellii 25 kDa (OmpV25)

Meesrikaew, P., Sanram, S., Robinson, R., Suginta, W.

To be published.

Macromolecule Content

Total Structure Weight: 98.57 kDa
Atom Count: 6,855
Modeled Residue Count: 840
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Porin	A, B, C, D	210	Vibrio harveyi	Mutation(s): 0 Gene Names: GalP Membrane Entity: Yes
UniProt
Find proteins for K5UDK4 (Vibrio harveyi) Explore K5UDK4 Go to UniProtKB: K5UDK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K5UDK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C8E (Subject of Investigation/LOI) Query on C8E Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Z [auth D]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain S [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain S [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain S [auth B]	S [auth B], Y [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Focus chain Y [auth C] Interactions & Density Focus chain S [auth B] Focus chain Y [auth C]