8JAE

Crystal structure of E33A mutant human galectin-10 produced by cell-free protein synthesis in complex with melezitose

PDB DOI: https://doi.org/10.2210/pdb8JAE/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Triticum aestivum
Mutation(s): Yes

Deposited: 2023-05-05 Released: 2024-05-08
Deposition Author(s): Kojima, M., Ueno, T., Abe, S., Hirata, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.222
R-Value Work: 0.194
R-Value Observed: 0.196

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cell-free protein crystallization for rapid structure determination of multiple substrates

Kojima, M., Abe, S., Hirata, K., Ueno, T.

To be published.

Macromolecule Content

Total Structure Weight: 16.92 kDa
Atom Count: 1,365
Modelled Residue Count: 140
Deposited Residue Count: 142
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-10	A	142	Homo sapiens	Mutation(s): 1 Gene Names: CLC, LGALS10, LGALS10A
UniProt & NIH Common Fund Data Resources
Find proteins for Q05315 (Homo sapiens) Explore Q05315 Go to UniProtKB: Q05315
PHAROS: Q05315 GTEx: ENSG00000105205
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05315
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-2)-[alpha-D-glucopyranose-(1-3)]beta-D-fructofuranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G80689JY GlyCosmos: G80689JY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.222
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.16	α = 90
b = 49.16	β = 90
c = 262.56	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2024-05-08
Type: Initial release
Version 1.1: 2024-07-17
Changes: Source and taxonomy

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 R01GM133198.