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

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Basic information

Entry
Database: PDB / ID: 5tib
TitleGasdermin-B C-terminal domain containing the polymorphism residues Arg299:Ser306 fused to maltose binding protein
ComponentsSugar ABC transporter substrate-binding protein,Gasdermin-B
KeywordsLIPID BINDING PROTEIN / alpha helices / fusion protein / C-terminal domain / 2 SNPs
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 / killing of cells of another organism ...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 / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / ACETATE ION / : / Gasdermin-B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsChao, 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 1, 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 / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,9396
Polymers122,1722
Non-polymers7674
Water5,152286
1
A: Sugar ABC transporter substrate-binding protein,Gasdermin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5114
Polymers61,0861
Non-polymers4243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sugar ABC transporter substrate-binding protein,Gasdermin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4292
Polymers61,0861
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.060, 104.060, 252.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsMonomer as determined by size exclusion chromatography

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Components

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


Mass: 61086.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli, Homo sapiens / Gene: malE, OO96_18925, GSDMB, GSDML, PP4052, PRO2521 / Plasmid: 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.: 2
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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence of this entry corresponds to a common polymorphism present in half of the population.

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 2.2 M sodium malonate, and 9 mM hexamine CoCl3 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→96.2 Å / Num. obs: 41354 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.6

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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: PDB 3H4Z

3h4z


Resolution: 2.6→96.19 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.403 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.482 / ESU R Free: 0.275
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 2166 5 %RANDOM
Rwork0.1836 ---
obs0.1861 41354 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.02 Å2 / Biso mean: 45.815 Å2 / Biso min: 4.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-0 Å2
2--0.85 Å2-0 Å2
3----1.71 Å2
Refinement stepCycle: final / Resolution: 2.6→96.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7901 0 51 286 8238
Biso mean--38.07 36.26 -
Num. residues----1063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198120
X-RAY DIFFRACTIONr_bond_other_d0.0070.027611
X-RAY DIFFRACTIONr_angle_refined_deg1.491.97511063
X-RAY DIFFRACTIONr_angle_other_deg1.023317487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57751057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66825.644326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.281151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1751522
X-RAY DIFFRACTIONr_chiral_restr0.0960.21283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219296
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021710
X-RAY DIFFRACTIONr_mcbond_it4.114.6784246
X-RAY DIFFRACTIONr_mcbond_other4.114.6784245
X-RAY DIFFRACTIONr_mcangle_it6.1976.9975297
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 171 -
Rwork0.254 2959 -
all-3130 -
obs--100 %

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