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- PDB-8srz: Structure of a bacterial death-like domain from Lysobacter enzymogenes -

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Basic information

Entry
Database: PDB / ID: 8srz
TitleStructure of a bacterial death-like domain from Lysobacter enzymogenes
ComponentsProbable serine protease FE772_23065
KeywordsIMMUNE SYSTEM / death fold / scaffold / adaptor / CARD / PYD / DD / DED / programmed cell death / pyroptosis
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / defense response to virus / proteolysis / plasma membrane
Similarity search - Function
Trypsin-like peptidase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable serine protease FE772_23065
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 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: Probable serine protease FE772_23065
B: Probable serine protease FE772_23065


Theoretical massNumber of molelcules
Total (without water)20,6032
Polymers20,6032
Non-polymers00
Water5,855325
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)58.252, 58.252, 122.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Probable serine protease FE772_23065 / Trypsin-like protease 2


Mass: 10301.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Gene: FE772_23065, Ga0399710_4915, GLE_4745 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0S2DN74, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 291 K / Method: vapor diffusion, hanging drop / Details: 4 M sodium formate

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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 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.25→46.64 Å / Num. obs: 64141 / % possible obs: 99 % / Redundancy: 17.3 % / CC1/2: 1 / Rpim(I) all: 0.014 / Net I/σ(I): 23
Reflection shellResolution: 1.25→1.27 Å / Num. unique obs: 64141 / CC1/2: 0.881

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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: 1.25→38.92 Å / SU ML: 0.1257 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1776 1996 3.12 %
Rwork0.1586 62042 -
obs0.1591 64038 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.35 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 0 325 1725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02041434
X-RAY DIFFRACTIONf_angle_d1.54871948
X-RAY DIFFRACTIONf_chiral_restr0.1074206
X-RAY DIFFRACTIONf_plane_restr0.0204258
X-RAY DIFFRACTIONf_dihedral_angle_d13.1024510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.25271380.22784294X-RAY DIFFRACTION96.31
1.28-1.320.21961400.19964360X-RAY DIFFRACTION97.15
1.32-1.350.21211410.19324413X-RAY DIFFRACTION97.98
1.35-1.40.18491410.20274362X-RAY DIFFRACTION98.34
1.4-1.450.23981380.19024393X-RAY DIFFRACTION98.52
1.45-1.510.18941400.17154439X-RAY DIFFRACTION98.81
1.51-1.570.15461430.15594469X-RAY DIFFRACTION99.18
1.57-1.660.17061430.15894430X-RAY DIFFRACTION99.39
1.66-1.760.17861510.16014462X-RAY DIFFRACTION99.59
1.76-1.90.19141440.16744435X-RAY DIFFRACTION99.74
1.9-2.090.17111430.15384499X-RAY DIFFRACTION99.85
2.09-2.390.16521450.14334468X-RAY DIFFRACTION99.98
2.39-3.010.1861430.15864499X-RAY DIFFRACTION100
3.01-38.920.16681460.15064519X-RAY DIFFRACTION99.74
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)
10.1134129513210.026647506303-0.002830561770990.314925352457-0.1120634357660.08222648371830.1019306133180.193233889399-0.362483837163-0.333573055314-0.02755072130020.15421983330.4821132381040.3880379727750.007101431044510.2287916327610.0632827961067-0.01162354833760.197656381677-0.02436078926830.2035737968858.5203211544621.261185923137.4172935795
20.193076047669-0.0656938149441-0.114925557202-0.001252685321150.007627697625270.392346414044-0.0521068467138-0.02286209748560.0207101013320.02456062399440.01228296690750.0185054563132-0.283901977411-0.0272106720956-6.8048625756E-50.1539266594740.00736198601883-0.0147419250770.1275603238680.006074904391650.1394620072614.7574951283633.502979874845.4811666024
30.44617851902-0.1189003575460.3339825105840.4929464299080.2159635205180.512230594482-0.02171234645160.126805188733-0.0194691245561-0.0703042136335-0.00602128226542-0.09459764385130.1904549819790.438449542225-0.0005734407506180.1321170977750.0213571452484-0.005647979226130.1943353674350.01632028055580.1522798150913.653880254426.30493678847.2754968023
40.191468968044-0.0388527388070.1468803491040.05242084172680.08102683030430.1921717862-0.06765825506430.058835839785-0.08514847302230.000993086003418-0.01050313223520.08782579035680.0511588476418-0.0519527309633-0.01477840020590.1196639304280.00953435209567-0.01511567655720.130096164762-0.002308183620510.134563525208-1.6235277719928.757472453246.757149488
50.6032885670050.266009131988-0.2663502542610.124674437124-0.01049088964051.00730085563-0.1218979667350.1926375146360.0625390379701-0.09398298794980.02949553248340.02928436940510.0222097719081-0.0572470306133-0.1273477560880.167145980901-0.0255672954731-0.06224578037210.159727007796-0.01006827706440.171357462851-6.1098350207827.571452967138.1049589508
60.133889109986-0.0907699559282-0.09380746288610.0943334877030.05679500773130.11997176908-0.0819298937831-0.0712024584056-0.257227843120.1118742631150.0198906297084-0.02504023469920.133787023302-0.106558867555-0.0003102911148680.164123524148-0.009151441233340.02822190883870.1814062306650.00736258653630.172247705641-4.5567009954825.271219218171.2431534745
70.0477041303512-0.04731720591550.02775999962770.105909417278-0.1276633913670.195536249944-0.03714241075010.01175691611740.07078929200660.00513385466368-0.01507083782150.0237060063842-0.116415023610.0151521813304-5.46003000063E-50.155638344502-0.0133770752054-0.01045333010730.144004362679-0.01485097082440.164037480495-0.81445324369634.964778634460.4642233182
80.2547629708950.0704564399196-0.08259144490280.6401450520940.01389382189290.329115187665-0.1112916118020.1304257268660.168496904903-0.150633182065-0.0345063655840.3648122917350.014781463617-0.287975901360.01140248077660.135344124129-0.0215456390934-0.01612371499180.167417257054-0.02516842551480.232329760334-12.059476095830.934541283257.3754866754
90.2054504125430.03272987284780.03252932407160.06643208710420.07376362787490.111262542056-0.0748895339102-0.009409118261230.0540416421325-0.126678245183-0.001690479881090.2169086743450.0399407267711-0.262521407425-0.0001990512973250.173120492108-0.0320300550939-0.01175263356070.168586068101-0.001345024619940.173504668139-8.8334200236326.480504069463.646981659
100.351905273836-0.3454015825240.0170895672820.17695976184-0.0341934240140.520438940273-0.0426797374866-0.0249121857576-0.0995122938544-0.0218313793610.040380037134-0.104681758470.0804626639920.0821725331218-0.0007102509977650.1368316791390.0125173112867-0.01452306129160.1704895318990.01306669511550.1458973684387.0381435905427.756810033865.5062430769
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 13 )AA4 - 131 - 10
22chain 'A' and (resid 14 through 30 )AA14 - 3011 - 27
33chain 'A' and (resid 31 through 62 )AA31 - 6228 - 59
44chain 'A' and (resid 63 through 76 )AA63 - 7660 - 73
55chain 'A' and (resid 77 through 91 )AA77 - 9174 - 88
66chain 'B' and (resid 4 through 15 )BB4 - 151 - 12
77chain 'B' and (resid 16 through 30 )BB16 - 3013 - 27
88chain 'B' and (resid 31 through 48 )BB31 - 4828 - 45
99chain 'B' and (resid 49 through 62 )BB49 - 6246 - 59
1010chain 'B' and (resid 63 through 91 )BB63 - 9160 - 88

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