5IO8

Salmonella Typhimurium VirG-like (STV) protein at 2.19 Angstrom resolution solved by Iodine SAD.

PDB DOI: https://doi.org/10.2210/pdb5IO8/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-03-08 Released: 2017-03-15
Deposition Author(s): Pandey, N.K., Ray, S., Suar, M., Bhavesh, N.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.245 (Depositor), 0.270 (DCC)
R-Value Work:
0.204 (Depositor), 0.230 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Salmonella Typhimurium VirG-like (STV) protein at at 2.19 Angstrom resolution by SAD.

Pandey, N.K., Ray, S., Suar, M., Bhavesh, N.S.

To be published.

Macromolecule Content

Total Structure Weight: 28.58 kDa
Atom Count: 1,683
Modelled Residue Count: 205
Deposited Residue Count: 232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VirG-like protein	A, B	116	Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344	Mutation(s): 0 Gene Names: SL1344_RS01575
UniProt
Find proteins for A0A0H3ND95 (Salmonella typhimurium (strain SL1344)) Explore A0A0H3ND95 Go to UniProtKB: A0A0H3ND95
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3ND95
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] 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 Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] 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 Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	N [auth A], O [auth A], P [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain X [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain X [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain X [auth B]	J [auth A], K [auth A], L [auth A], M [auth A], X [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.245 (Depositor), 0.270 (DCC)
R-Value Work: 0.204 (Depositor), 0.230 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.115	α = 90
b = 60.277	β = 90
c = 62.603	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-15

Deposition Author(s):

Funding Organization	Location	Grant Number
	India	--

Revision History (Full details and data files)

Version 1.0: 2017-03-15
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations, Refinement description