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- PDB-8g32: Pro-form of a CDCL short from E. anophelis -

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Basic information

Entry
Database: PDB / ID: 8g32
TitlePro-form of a CDCL short from E. anophelis
ComponentsThiol-activated cytolysin family protein
KeywordsTOXIN / pore-forming toxin / cholesterol-dependent cytolysin like / Elizabethkingia anophelis
Function / homologyThiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / cholesterol binding / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Thiol-activated cytolysin family protein
Function and homology information
Biological speciesElizabethkingia anophelis Ag1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJohnstone, B.A. / Christie, M.P. / Morton, C.J. / Parker, M.W.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160101874 Australia
Australian Research Council (ARC)DP200102871 Australia
CitationJournal: Nat Commun / Year: 2024
Title: Distant relatives of a eukaryotic cell-specific toxin family evolved a complement-like mechanism to kill bacteria.
Authors: Abrahamsen, H.L. / Sanford, T.C. / Collamore, C.E. / Johnstone, B.A. / Coyne, M.J. / Garcia-Bayona, L. / Christie, M.P. / Evans, J.C. / Farrand, A.J. / Flores, K. / Morton, C.J. / Parker, M. ...Authors: Abrahamsen, H.L. / Sanford, T.C. / Collamore, C.E. / Johnstone, B.A. / Coyne, M.J. / Garcia-Bayona, L. / Christie, M.P. / Evans, J.C. / Farrand, A.J. / Flores, K. / Morton, C.J. / Parker, M.W. / Comstock, L.E. / Tweten, R.K.
History
DepositionFeb 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 26, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol-activated cytolysin family protein
B: Thiol-activated cytolysin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,87813
Polymers78,9882
Non-polymers89011
Water7,170398
1
A: Thiol-activated cytolysin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0648
Polymers39,4941
Non-polymers5707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol-activated cytolysin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8145
Polymers39,4941
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.629, 171.629, 61.334
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thiol-activated cytolysin family protein


Mass: 39494.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis Ag1 (bacteria)
Gene: JCR23_19030 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7T7HCZ8

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Non-polymers , 7 types, 409 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.3 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.1 M Bis-Tris pH 6.4, 0.1 M sodium chloride, 1.75 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→74.32 Å / Num. obs: 88308 / % possible obs: 98.02 % / Redundancy: 29.7 % / Biso Wilson estimate: 21.32 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2147 / Rpim(I) all: 0.03967 / Rrim(I) all: 0.2184 / Net I/σ(I): 13.61
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 18.3 % / Mean I/σ(I) obs: 1.58 / Num. unique obs: 8759 / CC1/2: 0.623 / Rpim(I) all: 0.5924 / % possible all: 92.83

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Processing

Software
NameVersionClassification
DIALSdata reduction
xia2data reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
PHENIX1.17_3644refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→74.32 Å / SU ML: 0.1494 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.6565
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1799 1950 2.25 %
Rwork0.1617 84626 -
obs0.1621 86576 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.49 Å2
Refinement stepCycle: LAST / Resolution: 1.85→74.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4973 0 52 398 5423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01165173
X-RAY DIFFRACTIONf_angle_d1.0477032
X-RAY DIFFRACTIONf_chiral_restr0.0668814
X-RAY DIFFRACTIONf_plane_restr0.0073906
X-RAY DIFFRACTIONf_dihedral_angle_d12.63991861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.25921330.27225638X-RAY DIFFRACTION92.54
1.9-1.950.25381270.22965743X-RAY DIFFRACTION93.81
1.95-2.010.21211340.1925832X-RAY DIFFRACTION95.39
2.01-2.070.16651360.17226002X-RAY DIFFRACTION97.55
2.07-2.140.18921390.15975995X-RAY DIFFRACTION97.96
2.14-2.230.16961390.14936062X-RAY DIFFRACTION98.62
2.23-2.330.18851390.15326060X-RAY DIFFRACTION98.52
2.33-2.450.17261420.15246106X-RAY DIFFRACTION99.17
2.45-2.610.20461440.1546094X-RAY DIFFRACTION99.28
2.61-2.810.17571360.16236142X-RAY DIFFRACTION99.59
2.81-3.090.17041420.15526181X-RAY DIFFRACTION99.87
3.09-3.540.15311430.15336167X-RAY DIFFRACTION99.95
3.54-4.460.15611470.13736234X-RAY DIFFRACTION100
4.46-74.320.19331490.176370X-RAY DIFFRACTION99.91
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)
11.99719569417-1.13354937061-0.2532089385952.692752125941.200261029531.523348948780.1903024765120.074944136891-0.154581019853-0.271633958183-0.2477716757940.178892509346-0.04878848894630.1997246453230.1016765949920.1368435830330.04042106906810.03894492352230.2402753422980.02837944645170.10924816894133.204191565574.5165377901-0.138182073105
20.731028990874-0.8266516342550.09972504547493.63205566294-0.2296822571220.892720455524-0.003396209781380.0454477947384-0.0240357059326-0.167201538741-0.035689878507-0.1465984195080.04883261206590.148727056090.03740520795590.1151501997270.0279966888442-0.003621658917320.200691804904-0.006898998840340.15539598293327.751819757971.320413986313.0750563902
31.91210167185-0.9661079571740.9290875392072.26842113021-1.00821451732.44560694793-0.191839387255-0.252062044503-0.03303009851110.4440560051330.1682555043740.00602531525357-0.121470645888-0.01853377115810.02374415996490.1818420323540.04088415162470.01773423864740.1997726115812.18366629691E-50.13359615017822.700730682571.926576254528.5631396825
40.924309837319-0.506155163350.01096015634930.927931623759-0.1299259176130.9867610248960.04822015422450.106889044795-0.078704033062-0.104669425401-0.05798358430780.07658734876410.04094562298610.01710658378620.0005405930987110.1249430271750.0157613073251-0.01970293809210.148305220414-0.02898053217320.12351704467318.402612330676.11082202517.79257271138
52.818123505581.472227328950.1339826974242.0869372664-0.1881815271961.427393050230.0732485754828-0.211063617533-0.03899907853650.299792637695-0.164353965381-0.5642958705170.1611547075390.423477633470.05795446411090.2385335049010.0684524078085-0.06268264198220.2614852491060.01059932363680.38277283298233.906190382597.759694378215.0433955183
64.231308945971.831866163420.7550816053911.817293872160.9209901358413.417927504130.0596039695768-0.0163369246890.335069602349-0.04152922681190.0140280832622-0.767124049809-0.252619939140.511751496669-0.05849781834810.2305113217110.003980648015190.04850909998990.2990756291380.03365108673940.67249060632343.1987169363112.7784844764.83221256444
72.06100267330.628472276514-1.823997865392.79446574381-1.520415249544.912666311920.03371173728510.2115313798150.245567249328-0.30210035434-0.0420929812316-0.3100024584940.01261529562670.03195981107090.02686696658580.1838848333930.06571024788380.04123992867950.1227989185810.02093191331170.27309020630927.7012086654106.0716922313.81689213249
81.778497690390.376424256491-0.4192869503691.59520188848-0.601571201222.388364884480.0750382312501-0.3232973526470.3003824854650.381320188839-0.101855707334-0.363646809538-0.2750908932760.383715403702-0.04351104748980.278591300535-0.00978090468901-0.07899054825610.212544851956-0.05145116256910.34388992928929.5478266947107.6448977321.6037990003
91.20957269509-0.109526033602-0.1910358646211.36397260569-0.1698518562961.101850958940.05410981425560.01726832023780.2298460760690.125934819826-0.00245264416235-0.150006790646-0.1158638446540.0296206116323-0.06892477433960.1739490787110.01777113158210.002934815336370.110811664096-0.02431258234710.16948015869517.770115483107.30968275916.0271045356
101.64328795479-0.127455872038-0.678416584360.6772372983420.2439800643231.940872038450.0899408270255-0.229205957831-0.006569765960160.0625703579388-0.028806741318-0.5537978578160.2410773711060.479768157239-0.02443796780060.2010825292880.0186659510542-0.06022857477090.2312080795690.01966550809740.45463383213236.3896962644106.13741502910.4914775978
111.93749658506-0.6932132005581.431834452230.447183026278-0.6953548272182.82405279519-0.1480231289270.2752873786690.372874049171-0.0899274398799-0.0473191856442-0.878294836766-0.340827940351.072111859170.196698705020.337360529758-0.09147683681020.06193240401660.923825223909-0.08864142412551.2171739877157.7944022735112.3296858347.2167659345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 179 )
4X-RAY DIFFRACTION4chain 'A' and (resid 180 through 377 )
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 105 )
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 154 )
7X-RAY DIFFRACTION7chain 'B' and (resid 155 through 188 )
8X-RAY DIFFRACTION8chain 'B' and (resid 189 through 238 )
9X-RAY DIFFRACTION9chain 'B' and (resid 260 through 342 )
10X-RAY DIFFRACTION10chain 'B' and (resid 343 through 377 )
11X-RAY DIFFRACTION11chain 'B' and (resid 239 through 259 )

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