6TRG

Salmonella typhimurium neuraminidase mutant (D100S)

PDB DOI: https://doi.org/10.2210/pdb6TRG/pdb

Classification: HYDROLASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-12-18 Released: 2020-01-22
Deposition Author(s): Garman, E.F., Salinger, M.T., Murray, J.W., Laver, W.G., Kuhn, P., Vimr, E.R.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.116
R-Value Work: 0.101

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Salmonella typhimurium neuraminidase mutant (D100S)

Garman, E.F., Salinger, M.T., Murray, J.W., Laver, W.G., Kuhn, P., Vimr, E.R.

To be published.

Macromolecule Content

Total Structure Weight: 42.6 kDa
Atom Count: 3,836
Modelled Residue Count: 379
Deposited Residue Count: 379
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase	A [auth XXX]	379	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 1 Gene Names: nanH, STM0928 EC: 3.2.1.18
UniProt
Find proteins for P29768 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P29768 Go to UniProtKB: P29768
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29768
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth XXX] SDF format, chain J [auth XXX] MOL2 format, chain I [auth XXX] MOL2 format, chain J [auth XXX] mmCIF format, chain I [auth XXX] mmCIF format, chain J [auth XXX]	I [auth XXX], J [auth XXX]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth XXX] Focus chain J [auth XXX] Interactions & Density Focus chain I [auth XXX] Focus chain J [auth XXX]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth XXX] SDF format, chain H [auth XXX] SDF format, chain B [auth XXX] SDF format, chain C [auth XXX] SDF format, chain E [auth XXX] SDF format, chain F [auth XXX] SDF format, chain G [auth XXX] MOL2 format, chain D [auth XXX] MOL2 format, chain H [auth XXX] MOL2 format, chain B [auth XXX] MOL2 format, chain C [auth XXX] MOL2 format, chain E [auth XXX] MOL2 format, chain F [auth XXX] MOL2 format, chain G [auth XXX] mmCIF format, chain D [auth XXX] mmCIF format, chain H [auth XXX] mmCIF format, chain B [auth XXX] mmCIF format, chain C [auth XXX] mmCIF format, chain E [auth XXX] mmCIF format, chain F [auth XXX] mmCIF format, chain G [auth XXX]	B [auth XXX] C [auth XXX] D [auth XXX] E [auth XXX] F [auth XXX] B [auth XXX], C [auth XXX], D [auth XXX], E [auth XXX], F [auth XXX], G [auth XXX], H [auth XXX]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth XXX] Focus chain C [auth XXX] Focus chain D [auth XXX] Focus chain E [auth XXX] Focus chain F [auth XXX] Focus chain G [auth XXX] Focus chain H [auth XXX] Interactions & Density Focus chain B [auth XXX] Focus chain C [auth XXX] Focus chain D [auth XXX] Focus chain E [auth XXX] Focus chain F [auth XXX] Focus chain G [auth XXX] Focus chain H [auth XXX]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.116
R-Value Work: 0.101
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.17	α = 90
b = 81.636	β = 90
c = 91.148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
ACORN	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2020-01-22
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

Prepare Data

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Deposit Data

Help and Resources

6TRG

Salmonella typhimurium neuraminidase mutant (D100S)

Salmonella typhimurium neuraminidase mutant (D100S)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)