4YW4

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.214
R-Value Work: 0.182
R-Value Observed: 0.183

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a novel sialidase

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A182DW00
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 C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.214
R-Value Work: 0.182
R-Value Observed: 0.183
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

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

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

4YW4

Streptococcus pneumoniae sialidase NanC

Crystal structure of a novel sialidase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)