4XHB | pdb_00004xhb

Crystal structure of the NanB sialidase from streptococcus pneumoniae in complex with pentanediol and CHES

PDB DOI: https://doi.org/10.2210/pdb4XHB/pdb

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

Deposited: 2015-01-05 Released: 2016-01-27
Deposition Author(s): Brear, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.187 (Depositor), 0.191 (DCC)
R-Value Work:
0.150 (Depositor), 0.155 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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This is version 1.1 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: 73.83 kDa
Atom Count: 5,903
Modeled Residue Count: 658
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHE Query on NHE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
17Y Query on 17Y Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(1R,2S)-cyclopentane-1,2-diol C₅ H₁₀ O₂ VCVOSERVUCJNPR-SYDPRGILSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.187 (Depositor), 0.191 (DCC)
R-Value Work: 0.150 (Depositor), 0.155 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.494	α = 90
b = 82.585	β = 90
c = 117.193	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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Entry History

& Funding Information

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2016-01-27
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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.