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- PDB-5tj2: Gasdermin-B C-terminal domain containing the polymorphism residue... -

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Basic information

Entry
Database: PDB / ID: 5tj2
TitleGasdermin-B C-terminal domain containing the polymorphism residues Gly299:Ser306 fused to maltose binding protein
ComponentsSugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
KeywordsLIPID BINDING PROTEIN / alpha helices / fusion protein / C-terminal domain / 1 SNP
Function / homology
Function and homology information


cytotoxic T cell pyroptotic cell death / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / defense response to Gram-negative bacterium ...cytotoxic T cell pyroptotic cell death / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to bacterium / plasma membrane / cytoplasm
Similarity search - Function
Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain
Similarity search - Domain/homology
alpha-maltose / : / Gasdermin-B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsChao, L.K. / Herzberg, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM102810 United States
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2017
Title: Human Gasdermin-B and disease: Sulfatide Binding, Caspase cleavage, and Structural impact of Asthma- and IBS-Associated Polymorphism
Authors: Chao, L.K. / Kulakova, L. / Herzberg, O.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
B: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
C: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
D: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,2158
Polymers241,8464
Non-polymers1,3694
Water66737
1
A: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8042
Polymers60,4621
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8042
Polymers60,4621
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8042
Polymers60,4621
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8042
Polymers60,4621
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)144.039, 152.750, 255.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPROPROAA1 - 14061 - 553
21LYSLYSPROPROBB1 - 14061 - 553
12ILEILEALAALAAA2 - 14032 - 550
22ILEILEALAALACC2 - 14032 - 550
13LYSLYSGLYGLYAA1 - 14051 - 552
23LYSLYSGLYGLYDD1 - 14051 - 552
14ILEILEALAALABB2 - 14032 - 550
24ILEILEALAALACC2 - 14032 - 550
15LYSLYSGLYGLYBB1 - 14051 - 552
25LYSLYSGLYGLYDD1 - 14051 - 552
16ILEILEALAALACC2 - 14032 - 550
26ILEILEALAALADD2 - 14032 - 550

NCS ensembles :
ID
1
2
3
4
5
6
DetailsMonomer as determined by size exclusion chromatography

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Components

#1: Protein
Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein / Gasdermin-like protein


Mass: 60461.555 Da / Num. of mol.: 4 / Mutation: P1306S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, OO96_18925, GSDMB, GSDML, PP4052, PRO2521 / Plasmid: plasmid / Details (production host): pMALX(E) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178SBV6, UniProt: Q8TAX9
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6 / Details: 2.1 M sodium malonate, 10 mM EDTA / Temp details: room temperature

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→42.5 Å / Num. obs: 65695 / % possible obs: 99.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 11.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIB

5tib


Resolution: 2.8→42.5 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.354
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 3596 5.2 %RANDOM
Rwork0.2133 ---
obs0.2153 65695 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 239.9 Å2 / Biso mean: 64.283 Å2 / Biso min: 18.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0 Å2-0 Å2
2--2.65 Å20 Å2
3----1.77 Å2
Refinement stepCycle: final / Resolution: 2.8→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15746 0 92 37 15875
Biso mean--57.32 32.95 -
Num. residues----2127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916158
X-RAY DIFFRACTIONr_bond_other_d0.0070.0215121
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.97322031
X-RAY DIFFRACTIONr_angle_other_deg1.345334703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70352115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29625.603639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.656152459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7591543
X-RAY DIFFRACTIONr_chiral_restr0.0790.22569
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118520
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023403
X-RAY DIFFRACTIONr_mcbond_it5.0426.6178496
X-RAY DIFFRACTIONr_mcbond_other5.0416.6178495
X-RAY DIFFRACTIONr_mcangle_it7.9119.91810599
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A644820.07
12B644820.07
21A592660.07
22C592660.07
31A581840.07
32D581840.07
41B589560.08
42C589560.08
51B581860.08
52D581860.08
61C566000.07
62D566000.07
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 242 -
Rwork0.328 4801 -
all-5043 -
obs--99.23 %

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