6TVI

Salmonella typhimurium mutant neuraminidase (D100S)+ DANA

PDB DOI: https://doi.org/10.2210/pdb6TVI/pdb

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

Deposited: 2020-01-09 Released: 2020-02-12
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:
0.133 (Depositor), 0.140 (DCC)
R-Value Work:
0.118 (Depositor), 0.120 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Salmonella typhimurium mutant neuraminidase (D100S)+ DANA

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: 42.61 kDa
Atom Count: 3,852
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 AAA]	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 LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DAN Query on DAN Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain H [auth AAA]	H [auth AAA]	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID C₁₁ H₁₇ N O₈ JINJZWSZQKHCIP-UFGQHTETSA-N		Interactions Focus chain H [auth AAA] Interactions & Density Focus chain H [auth AAA]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth AAA] SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] MOL2 format, chain B [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain B [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA]	B [auth AAA] C [auth AAA] D [auth AAA] E [auth AAA] F [auth AAA] B [auth AAA], C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.133 (Depositor), 0.140 (DCC)
R-Value Work: 0.118 (Depositor), 0.120 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.068	α = 90
b = 81.781	β = 90
c = 91.065	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-12

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: 2020-02-12
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.3: 2024-11-20
Changes: Structure summary