5XN7 | pdb_00005xn7

Crystal structure of the effector domain RID of Vibrio vulnificus MARTX toxin

PDB DOI: https://doi.org/10.2210/pdb5XN7/pdb

Classification: TOXIN
Organism(s): Vibrio vulnificus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-05-18 Released: 2017-09-27
Deposition Author(s): Yin, L., Zhu, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.244 (Depositor), 0.242 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5XN7

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

Literature

Crystal structure of a MARTX toxin effector domain

Yin, L., Zhu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 137.97 kDa
Atom Count: 8,384
Modeled Residue Count: 1,096
Deposited Residue Count: 1,232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative RTX-toxin	A, B	616	Vibrio vulnificus	Mutation(s): 1 Gene Names: rtxA1 EC: 3.4.22
UniProt
Find proteins for A0A2S3R7M0 (Vibrio vulnificus) Explore A0A2S3R7M0 Go to UniProtKB: A0A2S3R7M0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S3R7M0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DIO Query on DIO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B]	H [auth A], I [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.244 (Depositor), 0.242 (DCC)
R-Value Work: 0.203 (Depositor)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.743	α = 90
b = 185.185	β = 95.6
c = 81.365	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81530068

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

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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.