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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.233 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

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

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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.233 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Chao, K., Herzberg, O.

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

Revision History  

• 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