4YW4 | pdb_00004yw4

Streptococcus pneumoniae sialidase NanC

• PDB DOI: https://doi.org/10.2210/pdb4YW4/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-20 Released: 2016-04-13 
• Deposition Author(s): Owen, C.D., Lukacik, P., Potter, J.A., Walsh, M., Taylor, G.L.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.214 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a novel sialidase

Owen, C.D., Lukacik, P., Potter, J.A., Walsh, M., Taylor, G.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 148.33 kDa 
• Atom Count: 10,872 
• Modeled Residue Count: 1,318 
• Deposited Residue Count: 1,318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase C	A, B	659	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: nanC, SPG_1219 EC: 3.2.1.18
UniProt
Find proteins for A0A182DW00 (Streptococcus pneumoniae) Explore A0A182DW00  Go to UniProtKB:  A0A182DW00

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.214 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.697	α = 90
b = 74.77	β = 95.71
c = 113.11	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Owen, C.D., Lukacik, P., Potter, J.A., Walsh, M., Taylor, G.L.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/F016778/1

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 2.0: 2017-08-30
  Changes: Atomic model, Author supporting evidence, Data collection
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description