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- PDB-8ss1: Structure of a bacterial death-like domain from Azospirillum sp. -

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Basic information

Entry
Database: PDB / ID: 8ss1
TitleStructure of a bacterial death-like domain from Azospirillum sp.
ComponentsSerine protease
KeywordsIMMUNE SYSTEM / death fold / scaffold / adaptor / CARD / PYD / DD / DED / programmed cell death / pyroptosis
Function / homologyPeptidase S1B / Trypsin-like peptidase domain / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / proteolysis / Serine protease
Function and homology information
Biological speciesAzospirillum sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsJohnson, A.G. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Biorxiv / Year: 2023
Title: CARD-like domains mediate anti-phage defense in bacterial gasdermin systems.
Authors: Wein, T. / Johnson, A.G. / Millman, A. / Lange, K. / Yirmiya, E. / Hadary, R. / Garb, J. / Steinruecke, F. / Hill, A.B. / Kranzusch, P.J. / Sorek, R.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease
B: Serine protease


Theoretical massNumber of molelcules
Total (without water)23,3042
Polymers23,3042
Non-polymers00
Water2,180121
1
A: Serine protease

B: Serine protease


Theoretical massNumber of molelcules
Total (without water)23,3042
Polymers23,3042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area1140 Å2
ΔGint-8 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.959, 65.367, 38.829
Angle α, β, γ (deg.)90.000, 111.061, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Serine protease /


Mass: 11652.190 Da / Num. of mol.: 2 / Fragment: Bacterial death-like domain, residues 13-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum sp. (bacteria) / Gene: TSO352_05040 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2U1VUZ9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES-KOH (pH 7.5), 200 mM ammonium acetate, and 25% 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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.88→36.24 Å / Num. obs: 14427 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 25.13 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.062 / Net I/σ(I): 7.7
Reflection shellResolution: 1.88→1.92 Å / Num. unique obs: 850 / CC1/2: 0.526

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→36.24 Å / SU ML: 0.2552 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.8714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 1441 10.11 %
Rwork0.2041 12817 -
obs0.2078 14258 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.94 Å2
Refinement stepCycle: LAST / Resolution: 1.88→36.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 0 121 1656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361559
X-RAY DIFFRACTIONf_angle_d0.61182100
X-RAY DIFFRACTIONf_chiral_restr0.0373227
X-RAY DIFFRACTIONf_plane_restr0.005278
X-RAY DIFFRACTIONf_dihedral_angle_d12.9077612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.940.37631290.28461156X-RAY DIFFRACTION88.74
1.94-2.020.28031470.24031251X-RAY DIFFRACTION96.88
2.02-2.110.27791420.22211295X-RAY DIFFRACTION98.56
2.11-2.230.26321420.20791294X-RAY DIFFRACTION99.79
2.23-2.370.26541450.20651295X-RAY DIFFRACTION99.65
2.37-2.550.27611460.20571292X-RAY DIFFRACTION99.04
2.55-2.80.29751470.20751292X-RAY DIFFRACTION99.65
2.8-3.210.2361390.20461295X-RAY DIFFRACTION99.31
3.21-4.040.19151490.18461314X-RAY DIFFRACTION99.8
4.04-36.240.2091550.19771333X-RAY DIFFRACTION99.6
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)
11.0691752946-0.590176295472-0.6533002762770.768631649606-0.03786521238280.708274170516-0.1049918828650.0750218333429-0.0350866621464-0.0158651386402-0.07950569036920.04311259708330.26663490835-0.13619336057-0.01576021238710.2644751937270.02273238696510.03222085100510.1967247670940.01540855871570.202621166164-4.48541454391-0.5421717761079.93725598285
20.581944145860.04142357639680.04796909196440.547397480322-0.02370795155240.423481783665-0.05909630067720.175366766138-0.129863260636-0.172875617691-0.107004094227-0.1397895169570.05409106006550.27804978362-0.1600243122790.500318548815-0.02371026360970.1799115739160.2560439837020.05792976829660.2805875617468.802204338521.3433773823.85051387802
31.7900946973-0.2958808027390.4386884243090.456862487801-0.3330363230370.719229943851-0.297791857959-0.2591716642050.4558346636860.05097557131810.0316032991181-0.4987863819550.04560715022880.175905006609-0.03475857041740.2948168415790.05447492595410.01630871846210.226828098401-0.01219778085650.2578564057875.112759418873.082298138312.1867057033
40.96067832079-0.1063478734030.3806282164131.0200898419-0.2904430072250.9048437157850.0859594373571-0.1291295452940.07586846327820.417323284707-0.07403328288770.5740081606830.130651565818-0.252922380678-0.03378797182290.3526753809970.007407130465790.0657692519390.211314915418-0.006116069288940.239502972435-10.6807337937-1.6428056804418.4626740358
50.2828009946280.279666548353-0.3076173170060.560523976855-0.03173692345880.5322970997510.5029377014920.21804086963-0.3098065665670.190657502341-0.128071787085-0.06508554529790.724318620580.269838437710.006591039160990.244582764770.03072247864860.008384740315350.240681683596-0.02317236144080.193074496508-13.2497578344-20.67734315-2.98695904223
60.0159767067090.0895583133527-0.219964741960.271932753173-0.1352911235150.1902379341050.184896397033-0.1799093134990.1903115618220.0458987160987-0.1436056342890.0938444218999-0.30728691105-0.0458567063907-3.64089359598E-50.3314359924760.001487702816720.06659795262120.221205812096-0.005301207959270.243312471318-16.5310463551-12.76073236959.63118521732
70.4039211401570.347463951081-0.2913256365490.478617223813-0.3954508164720.7727236718250.2720889244460.1370878935820.25133924246-0.150732790150.07550527646620.245897527857-0.603038486261-0.3781415902110.06995432558440.240977093345-0.03830595346870.02534045998740.187905866781-0.005854930765430.190938971923-18.4807687866-25.560744294513.1746201861
80.198132575792-0.223643138018-0.2454101330960.4998690403440.08078819439180.308890762635-0.0274826524388-0.22814455812-0.04160561381810.0965654287866-0.008408668073120.08673748999910.0178838504308-0.07532717064850.0009417014333720.374107207625-0.02698044373010.09960960575680.2760515407220.005327209881770.251304231552-18.3317148862-22.49124284324.52481343318
90.05789049458810.111729654958-0.1101229482940.5446535189580.3712317096480.731384292293-0.00231686079211-0.05448091817520.251258381503-0.3197262268830.135887649143-0.0997086779693-0.3508749017450.0850804628651-0.007187173099380.283498990848-0.001759925223950.01890259026470.2265255500630.01078022968260.255192548455-13.5325873334-11.138348272-0.671757259468
100.702865761608-0.0767979371002-0.2038353789180.3129186565950.1687180281090.185723712603-0.4434961940570.9065158548940.382705569329-0.5747751182080.5058853436220.357849876137-0.4000307992970.332681210459-0.005302432953930.47651078105-0.003816726702850.08466669023640.293489854137-0.03010551789040.249202546646-6.90545178532-15.4710675859-10.4076813098
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 12 through 43 )AA12 - 431 - 32
22chain 'A' and (resid 44 through 57 )AA44 - 5733 - 46
33chain 'A' and (resid 58 through 78 )AA58 - 7847 - 67
44chain 'A' and (resid 79 through 109 )AA79 - 10968 - 98
55chain 'B' and (resid 12 through 24 )BB12 - 241 - 13
66chain 'B' and (resid 25 through 43 )BB25 - 4314 - 32
77chain 'B' and (resid 44 through 63 )BB44 - 6333 - 46
88chain 'B' and (resid 64 through 78 )BB64 - 7847 - 61
99chain 'B' and (resid 79 through 96 )BB79 - 9662 - 79
1010chain 'B' and (resid 97 through 108 )BB97 - 10880 - 91

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