2F28 | pdb_00002f28

Crystal Structure of the Human Sialidase Neu2 Q116E Mutant

PDB DOI: https://doi.org/10.2210/pdb2F28/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2005-11-15 Released: 2006-11-21
Deposition Author(s): Chavas, L.M.G., Kato, R., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.216 (Depositor), 0.217 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2F28

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the Human Sialidase Neu2 Q116E Mutant

Chavas, L.M.G., Kato, R., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

To be published.

Macromolecule Content

Total Structure Weight: 42.49 kDa
Atom Count: 3,110
Modeled Residue Count: 358
Deposited Residue Count: 382
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase 2	A	382	Homo sapiens	Mutation(s): 1 EC: 3.2.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3R4 (Homo sapiens) Explore Q9Y3R4 Go to UniProtKB: Q9Y3R4
PHAROS: Q9Y3R4 GTEx: ENSG00000115488
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y3R4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.240 (Depositor), 0.241 (DCC)
R-Value Work: 0.216 (Depositor), 0.217 (DCC)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.66	α = 90
b = 145.66	β = 90
c = 64.4	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-11-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-21
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-10-25
Changes: Data collection, Refinement description
Version 1.5: 2024-10-30
Changes: Structure summary

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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.