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- PDB-7n51: Structure of a bacterial gasdermin from Vitiosangium sp. -

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Basic information

Entry
Database: PDB / ID: 7n51
TitleStructure of a bacterial gasdermin from Vitiosangium sp.
ComponentsGasdermin
KeywordsIMMUNE SYSTEM / gasdermin / immunity / membrane / pore-forming protein / lipid binding protein / palmitoylation
Function / homologydefense response to virus / plasma membrane / cytoplasm / Gasdermin bGSDM
Function and homology information
Biological speciesVitiosangium sp. GDMCC 1.1324 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 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 / Year: 2021
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.
History
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 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

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Assembly

Deposited unit
A: Gasdermin


Theoretical massNumber of molelcules
Total (without water)28,4951
Polymers28,4951
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.383, 87.383, 141.969
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Gasdermin


Mass: 28494.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitiosangium sp. GDMCC 1.1324 (bacteria)
Gene: DAT35_31115 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2T4VDM4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 90 mM HEPES-KOH (pH 7.5), 1.2 M tri-sodium citrate, and 10% glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.67→47.19 Å / Num. obs: 37407 / % possible obs: 100 % / Redundancy: 39.4 % / Biso Wilson estimate: 34.13 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.011 / Net I/σ(I): 28
Reflection shellResolution: 1.68→1.71 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1876 / CC1/2: 0.602 / Rpim(I) all: 0.74 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: SAD / Resolution: 1.67→41.76 Å / SU ML: 0.2001 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6403
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 1491 4 %
Rwork0.1936 35789 -
obs0.1945 37280 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.4 Å2
Refinement stepCycle: LAST / Resolution: 1.67→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 0 145 2134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062017
X-RAY DIFFRACTIONf_angle_d0.82952720
X-RAY DIFFRACTIONf_chiral_restr0.0561312
X-RAY DIFFRACTIONf_plane_restr0.0047355
X-RAY DIFFRACTIONf_dihedral_angle_d18.5864756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.730.40171210.38442948X-RAY DIFFRACTION92.16
1.73-1.790.33911340.34873216X-RAY DIFFRACTION99.73
1.79-1.860.36591330.29613201X-RAY DIFFRACTION99.94
1.86-1.950.2821350.23523222X-RAY DIFFRACTION99.88
1.95-2.050.23351340.20613220X-RAY DIFFRACTION99.85
2.05-2.180.24751350.18933237X-RAY DIFFRACTION99.82
2.18-2.350.241350.19423254X-RAY DIFFRACTION99.94
2.35-2.580.2291370.20593280X-RAY DIFFRACTION99.91
2.58-2.960.2351380.2123292X-RAY DIFFRACTION99.94
2.96-3.720.20491400.18353353X-RAY DIFFRACTION100
3.72-41.760.18711490.17153566X-RAY DIFFRACTION99.95
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)
11.88779774887-0.7261973441770.3341964704221.883354301730.01202075121771.77453788720.136863100588-0.162179463854-0.1054819600990.4112460655630.02117497531640.307508438586-0.1424373185430.0340342322567-0.1976113686620.431017526724-0.02175339361560.06214712169960.352031398495-0.03063773862770.38496302074213.738456097516.476798416650.6657877055
22.93298928681-3.029389410870.4105130784317.26460629789-0.1370444573016.624966964390.154412633287-1.1408499263-0.2765194089340.9138911211110.02544229164810.3875339981390.164899279234-0.127010747008-0.05452465987970.476857161494-0.05157955841680.03644063367780.478866973172-0.01197059776010.42303602315617.05712716172.8070901804360.4733556937
31.33597030054-0.9886228409790.2278209051982.777286981050.0961391516110.5321624792770.04515987507-0.02229058254580.2109468110670.193856947765-0.0606635748245-0.176685738036-0.1334907301850.185824484823-0.03834511555650.431652321326-0.07575796704310.05046586597310.454605644366-0.0194337873580.39840588165819.690239079318.649829745253.9380944569
42.25754552912-0.529489237489-0.2354975186193.481893718130.2426817998080.9841802010290.0881993760049-0.09536984874850.02946047580220.0695564552523-0.04265281691780.0324552710579-0.06050982606140.1448228075740.01669784521460.338805597965-0.04417777433850.02194449670650.405097049626-0.07414425524060.27854650689218.715598067913.383456909654.923736996
52.866577405180.6990312173790.1600470263692.21674158418-0.1427182599223.17235988781-0.00524561153571-0.2918986184310.8629264243990.215487477920.02214526373220.132084014796-0.535328436181-0.0775715095181-0.0641640581230.547301831578-0.08822213418530.05131848122730.441364789923-0.1101488847490.67162189460816.863059110137.014879606158.0493291131
60.2748239991990.402919381954-0.5233820461487.1411379152-0.4223896269111.672271051620.1507082028230.277110450118-0.0732735063245-0.849207777079-0.113520646532-0.2477683752650.04822708875950.02108966432440.00925035334230.4002512892630.0498642377393-0.05307108649770.431929361978-0.06776993135360.41267606029818.7417602116-2.6701390333546.4997140999
72.34365616767-0.980628109483-0.2126029862293.970634084840.2973186660082.56685686193-0.0130613766155-0.0251607793474-0.369159126710.146412318038-0.1576445934480.4195719854260.140786167433-0.1534935259210.04653926949360.409167592656-0.001137141397840.01303637363620.359980662311-0.03899478613530.46222993573715.01260160357.1796049499148.3020980582
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 1 through 30 )1 - 301 - 30
22chain 'A' and (resid 31 through 48 )31 - 4831 - 48
33chain 'A' and (resid 49 through 93 )49 - 9349 - 93
44chain 'A' and (resid 94 through 169 )94 - 16994 - 169
55chain 'A' and (resid 170 through 213 )170 - 213170 - 213
66chain 'A' and (resid 214 through 240 )214 - 240214 - 237
77chain 'A' and (resid 241 through 266 )241 - 266238 - 263

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