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- PDB-7n50: Structure of a bacterial gasdermin from Bradyrhizobium tropiciagri -

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Basic information

Entry
Database: PDB / ID: 7n50
TitleStructure of a bacterial gasdermin from Bradyrhizobium tropiciagri
ComponentsGasdermin
KeywordsIMMUNE SYSTEM / gasdermin / immunity / membrane / pore-forming protein / lipid binding protein / palmitoylation
Biological speciesBradyrhizobium tropiciagri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJohnson, A.G. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)T32CA207021 United States
Citation
Journal: Science / Year: 2022
Title: Bacterial gasdermins reveal an ancient mechanism of cell death.
Authors: Johnson, A.G. / Wein, T. / Mayer, M.L. / Duncan-Lowey, B. / Yirmiya, E. / Oppenheimer-Shaanan, Y. / Amitai, G. / Sorek, R. / Kranzusch, P.J.
#1: Journal: Biorxiv
Title: Bacterial gasdermins reveal and ancient mechanism of cell death
Authors: Johnson, A.G. / Wein, T. / Mayer, M.L. / Duncan-Lowey, B. / Yirmiya, E. / Oppenheimer-Shaanan, Y. / Amitai, G. / Sorek, R. / Kranzusch, P.J.
History
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gasdermin


Theoretical massNumber of molelcules
Total (without water)27,8191
Polymers27,8191
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.770, 146.180, 34.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-366-

HOH

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Components

#1: Protein Gasdermin


Mass: 27818.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium tropiciagri (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.87 Å3/Da / Density % sol: 34.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 100 mM sodium acetate (pH 4.4) and 23% PEG-3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→40.77 Å / Num. obs: 33993 / % possible obs: 98.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 18.03 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.038 / Net I/σ(I): 12.3
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1639 / CC1/2: 0.216 / Rpim(I) all: 0.787

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→39.27 Å / SU ML: 0.2052 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.0732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2202 3393 10.01 %
Rwork0.1879 30507 -
obs0.1909 33900 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.81 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 0 159 1982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871860
X-RAY DIFFRACTIONf_angle_d1.05172512
X-RAY DIFFRACTIONf_chiral_restr0.0697289
X-RAY DIFFRACTIONf_plane_restr0.0093327
X-RAY DIFFRACTIONf_dihedral_angle_d13.0531686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.33023230.29631213X-RAY DIFFRACTION94.8
1.52-1.540.31971330.27391202X-RAY DIFFRACTION97.02
1.54-1.570.33541370.26461226X-RAY DIFFRACTION95.85
1.57-1.590.25651400.24461265X-RAY DIFFRACTION99.22
1.59-1.620.27781360.22951220X-RAY DIFFRACTION96.31
1.62-1.650.25411390.22371252X-RAY DIFFRACTION98.23
1.65-1.680.27831380.21381235X-RAY DIFFRACTION97.51
1.68-1.720.22171370.21041237X-RAY DIFFRACTION97.65
1.72-1.750.23681410.19441274X-RAY DIFFRACTION98.47
1.75-1.80.19691390.19191243X-RAY DIFFRACTION97.32
1.8-1.840.24681420.1881267X-RAY DIFFRACTION98.6
1.84-1.890.2251380.18581222X-RAY DIFFRACTION98.27
1.89-1.950.23381390.19291295X-RAY DIFFRACTION97.62
1.95-2.010.22411420.19081241X-RAY DIFFRACTION99.93
2.01-2.080.20531400.17851279X-RAY DIFFRACTION98.13
2.08-2.160.19931400.17131280X-RAY DIFFRACTION98.61
2.16-2.260.21231390.16711271X-RAY DIFFRACTION99.09
2.26-2.380.21751590.17881280X-RAY DIFFRACTION99.65
2.38-2.530.20861440.17471296X-RAY DIFFRACTION98.77
2.53-2.730.23921320.18641303X-RAY DIFFRACTION99.17
2.73-30.20361460.17731304X-RAY DIFFRACTION99.66
3-3.430.20661490.17271317X-RAY DIFFRACTION99.59
3.43-4.330.18981500.17181348X-RAY DIFFRACTION100
4.33-39.270.22681580.19861437X-RAY DIFFRACTION99.5
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.589118969250.895738834103-0.564585924952.127889512340.3140160238763.37319156469-0.1327398638970.486934469829-0.0769239315233-0.7290148829760.1639246456140.22098403719-0.121470582542-0.5511388468110.05544317447130.26867510445-0.0367919599866-0.02612795860260.219692884571-0.004283260372710.14159797439717.077206435416.8167370217-7.84570036376
21.379398067420.4419386552180.6101506005852.42495721128-1.240208783442.297715141150.112021091373-0.247201822005-0.1496259034870.123257749106-0.02837770466920.1864287957910.0224054561597-0.203386190583-0.005622293727110.130587695779-0.00858532571912-0.01787940565670.1469489948110.02241504406810.18235696728914.801004146314.79715785879.73664093611
31.053766489740.855433285102-0.424824939281.21143879433-0.6939013326911.28797306878-0.01060990502970.0293004184194-0.0602821455088-0.118173186199-0.0241660866047-0.009640748348970.009665038641430.004829132310020.04268227430160.1180405057040.00257836597609-0.01237006897810.107606306627-0.01559388495660.10197483334420.80784336621.9447410558-3.00279060969
43.189266413330.549961167046-1.143933852081.663809216550.1792584037113.10282041298-0.0512028405822-0.0987932440928-0.0728074853253-0.06849907997140.03218502433570.4943569988670.0936322062051-0.4291117682980.1495939766810.0850277156049-0.01293454400820.003733035851230.1358040586980.04475483513390.2485964881018.637968922612.80916845389.60446857069
51.125982256240.219740616536-0.1940153016831.70705768191-0.9882421233012.975224087310.008648277312390.05774169289820.0341960569238-0.08892541159540.000652457914707-0.05102997641-0.09545339321120.3501654758470.01618176691640.132817152197-0.0349381806879-0.006090733811720.200761557815-0.0003728605576460.11537709856733.189275131531.4248108286-10.1057691951
61.775591612821.01656948823-1.415749185911.31397479873-0.8324776677112.06789307407-0.1600911575910.133805096288-0.254186803157-0.07635532484980.142601410920.1477630572030.103575640252-0.2035677271230.04248343630790.1211102193660.00184874140113-0.02329406475520.1300170995980.01647993373140.18168070300911.27529478514.1148608214.27615943133
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 24 )2 - 241 - 23
22chain 'A' and (resid 25 through 75 )25 - 7524 - 74
33chain 'A' and (resid 76 through 138 )76 - 13875 - 137
44chain 'A' and (resid 139 through 159 )139 - 159138 - 155
55chain 'A' and (resid 160 through 204 )160 - 204156 - 200
66chain 'A' and (resid 205 through 259 )205 - 259201 - 240

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