4XJU | pdb_00004xju

Crystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 4-acetamido-2-fluoro-3-hydroxy-6-[1,2-dihydroxyethyl]-7,8-dioxabicyclo[3.2.1]octane-1-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb4XJU/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-01-09 Released: 2016-01-13
Deposition Author(s): Brear, P.
Funding Organization(s): Biotechnology and Biological Sciences Research Council, SULSA

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.206 (Depositor), 0.227 (DCC)
R-Value Work:
0.170 (Depositor), 0.208 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

`The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB

Rogers, G.W., Brear, P., Yang, L., Chen, A.S., Mitchell, J.B.O., Taylor, G.L., Westwood, N.J.

To be published.

Macromolecule Content

Total Structure Weight: 74.24 kDa
Atom Count: 5,960
Modeled Residue Count: 658
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase B	A	658	Streptococcus pneumoniae TIGR4	Mutation(s): 1 Gene Names: nanB, SP_1687 EC: 3.2.1.18
UniProt
Find proteins for Q54727 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q54727 Go to UniProtKB: Q54727
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q54727
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
19D Query on 19D 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]	(1R,2R,3R,4R,5R,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-4-fluoro-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid C₁₁ H₁₆ F N O₈ JCWSZUBTEOFKAD-DAXAGCIGSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.206 (Depositor), 0.227 (DCC)
R-Value Work: 0.170 (Depositor), 0.208 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.414	α = 90
b = 82.418	β = 90
c = 116.697	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Brear, P.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--
SULSA	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 2.0: 2017-08-30
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description