5TIB | pdb_00005tib

Gasdermin-B C-terminal domain containing the polymorphism residues Arg299:Ser306 fused to maltose binding protein

PDB DOI: https://doi.org/10.2210/pdb5TIB/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Escherichia coli, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-10-01 Released: 2017-02-01
Deposition Author(s): Chao, K., Herzberg, O.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.233 (Depositor), 0.186 (DCC)
R-Value Work:
0.184 (Depositor), 0.191 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Human Gasdermin-B and disease: Sulfatide Binding, Caspase cleavage, and Structural impact of Asthma- and IBS-Associated Polymorphism

Chao, L.K., Kulakova, L., Herzberg, O.

(2017) Proc Natl Acad Sci U S A

DOI: https://doi.org/10.1073/pnas.1616783114

Macromolecule Content

Total Structure Weight: 122.94 kDa
Atom Count: 8,238
Modeled Residue Count: 1,063
Deposited Residue Count: 1,114
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter substrate-binding protein,Gasdermin-B	A, B	557	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: malE, OO96_18925
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAX9 (Homo sapiens) Explore Q8TAX9 Go to UniProtKB: Q8TAX9
PHAROS: Q8TAX9 GTEx: ENSG00000073605
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TAX9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.233 (Depositor), 0.186 (DCC)
R-Value Work: 0.184 (Depositor), 0.191 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.06	α = 90
b = 104.06	β = 90
c = 252.21	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Chao, K.

Herzberg, O.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM102810

Revision History (Full details and data files)

Version 1.0: 2017-02-01
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2017-11-01
Changes: Author supporting evidence
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary