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- PDB-3g4n: Crystal structure of the activated aerolysin mutant H132D -

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Basic information

Entry
Database: PDB / ID: 3g4n
TitleCrystal structure of the activated aerolysin mutant H132D
ComponentsAerolysin
KeywordsTOXIN / CYTOLYTIC TOXIN / PORE-FORMING TOXIN / Membrane / Secreted
Function / homology
Function and homology information


toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
Proaerolysin; Chain A, domain 2 / Proaerolysin, chain A, domain 2 / Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Proaerolysin, chain A, domain 3 / Aerolysin / Aerolysin toxin / Aerolysin toxin / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily ...Proaerolysin; Chain A, domain 2 / Proaerolysin, chain A, domain 2 / Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Proaerolysin, chain A, domain 3 / Aerolysin / Aerolysin toxin / Aerolysin toxin / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain / Proaerolysin; Chain A, domain 3 / Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / C-type lectin fold / Beta Complex / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPernot, L. / Schiltz, M. / van der Goot, G.
Citation
Journal: Plos Pathog. / Year: 2011
Title: Dual chaperone role of the C-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin.
Authors: Iacovache, I. / Degiacomi, M.T. / Pernot, L. / Ho, S. / Schiltz, M. / Dal Peraro, M. / van der Goot, F.G.
#1: Journal: Nature / Year: 1994
Title: Structure of the Aeromonas toxin proaerolysin in its water-soluble and membrane-channel states.
Authors: Parker, M.W. / Buckley, J.T. / Postma, J.P. / Tucker, A.D. / Leonard, K. / Pattus, F. / Tsernoglou, D.
History
DepositionFeb 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aerolysin
B: Aerolysin


Theoretical massNumber of molelcules
Total (without water)103,9152
Polymers103,9152
Non-polymers00
Water6,143341
1
A: Aerolysin


Theoretical massNumber of molelcules
Total (without water)51,9571
Polymers51,9571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aerolysin


Theoretical massNumber of molelcules
Total (without water)51,9571
Polymers51,9571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.723, 70.211, 165.446
Angle α, β, γ (deg.)90.00, 109.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aerolysin


Mass: 51957.395 Da / Num. of mol.: 2 / Mutation: H132D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: aerA / Plasmid: PET22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09167
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) 17%-19%, SODIUM ACETATE 50mM pH 5.4 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9536 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.1→55.927 Å / Num. obs: 59799 / % possible obs: 98.6 % / Redundancy: 21.2 % / Biso Wilson estimate: 34.21 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.085 / Net I/σ(I): 27.43
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 4.86 / Num. unique all: 8607 / Rsym value: 0.368 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PRE

1pre


Resolution: 2.1→55.902 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / Cross valid method: THROUGHOUT / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 3017 5.05 %Random
Rwork0.2138 ---
obs0.2162 59753 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.868 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 160.84 Å2 / Biso mean: 48.92 Å2 / Biso min: 9.12 Å2
Baniso -1Baniso -2Baniso -3
1--6.3272 Å20 Å21.9398 Å2
2--19.0791 Å2-0 Å2
3----12.752 Å2
Refinement stepCycle: LAST / Resolution: 2.1→55.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6885 0 0 341 7226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077094
X-RAY DIFFRACTIONf_angle_d1.0359674
X-RAY DIFFRACTIONf_chiral_restr0.0721019
X-RAY DIFFRACTIONf_plane_restr0.0051262
X-RAY DIFFRACTIONf_dihedral_angle_d19.0892479
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.13280.33271420.2674254297
2.1328-2.16780.29371470.2366250397
2.1678-2.20520.27171390.2352255697
2.2052-2.24530.32111330.2249250598
2.2453-2.28850.30431270.2245260198
2.2885-2.33520.29741400.2279251998
2.3352-2.38590.31071450.2119255298
2.3859-2.44140.31151260.2154253398
2.4414-2.50250.31021370.2184257098
2.5025-2.57020.32561370.2269258298
2.5702-2.64580.30041330.2334256298
2.6458-2.73120.31111220.2331257998
2.7312-2.82880.2744990.2351267199
2.8288-2.94210.28511290.2342255999
2.9421-3.07590.2731480.2204256099
3.0759-3.23810.25131550.2294256599
3.2381-3.4410.29261300.2201263099
3.441-3.70660.24011500.2084260999
3.7066-4.07950.23661400.1899257999
4.0795-4.66950.19831380.1601262399
4.6695-5.88210.21500.1637264799
5.8821-55.94720.20561500.1814268999
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)
10.93820.3674-0.53421.46240.97830.3277-0.01410.65250.0285-0.33910.22020.0752-0.8061-0.5796-0.1680.39650.0984-0.05550.20040.05060.2132-20.767415.459135.0698
20.293-0.1654-0.30.1059-0.05742.2353-0.047-0.0624-0.0299-0.07320.10830.13590.1523-0.3705-0.06640.1884-0.0238-0.0380.25560.06280.1636-18.5039-1.009627.5278
30.6674-0.26780.1854-0.0557-0.28210.1851-0.095-0.0691-0.108-0.0675-0.01140.09450.27890.16410.10230.53770.0125-0.07760.34490.05350.2316-5.3296-14.272616.3054
40.5749-0.80660.5780.5965-0.4453-0.095-0.10610.02910.08080.09540.0495-0.0115-0.22770.25040.05790.40290.00930.03940.23380.08630.19066.0845-15.994162.1146
51.56170.3565-0.34730.76950.02091.1190.506-0.92-0.068-0.1073-0.49950.2171-0.81911.06870.0740.5011-0.01730.03650.71110.00760.2932.9782-13.0142.5851
60.66-0.4985-0.205-0.0209-0.17330.43940.11270.00740.34590.26450.3433-0.2494-0.4421-0.2337-0.26990.65080.19090.0680.3979-0.00280.38346.5281-10.417470.8032
7-0.5139-0.115-0.00620.5659-0.64760.3202-0.09890.0224-0.0164-0.16050.17330.05820.14-0.2623-0.12880.26340.1196-0.04380.43190.11180.1951-2.6864-14.560240.6607
80.7220.3564-0.12310.06350.15620.38160.0225-0.03360.1412-0.31130.00410.047-0.03570.191-0.01640.4351-0.0583-0.06160.35380.06370.1765-12.95565.189111.6168
90.2222-0.13030.38020.4665-0.56590.9764-0.01010.05260.0406-0.02510.0466-0.0821-0.27170.0059-0.0460.24360.1518-0.01040.26280.0340.23026.1669-17.71865.5437
101.2984-0.0119-0.81411.2336-0.39950.8340.1513-0.5867-0.31140.0887-0.05250.2472-0.85830.9035-0.05560.4124-0.1339-0.01720.2143-0.04350.1279-6.410314.283548.0667
110.8444-0.451-0.54120.2157-0.21830.8408-0.01510.1563-0.0664-0.0417-0.0558-0.0463-0.07710.6780.03210.2283-0.14910.01650.4842-0.00580.1756-3.40659.993940.1377
120.76310.39450.0840.31-0.10470.0225-0.2270.2108-0.523-0.01060.2121-0.01470.24770.42470.01230.15540.07960.04420.0714-0.05150.3865-14.3542-18.068266.8024
131.0456-0.0468-0.00250.72050.04740.4844-0.31620.1067-0.48190.01910.01850.09160.3387-0.13780.27620.219-0.05010.110.1222-0.08430.4312-21.2261-18.914662.8241
140.9824-0.535-0.53621.96820.54131.54710.53890.3725-0.1188-1.24140.00051.1298-0.92240.0107-0.09081.1315-0.153-0.17930.70170.01990.6516-32.7189-10.20137.3345
151.25880.301-0.55460.7134-0.52650.8388-0.34530.71860.1138-0.13950.46420.0110.3715-1.0421-0.0590.3952-0.34370.10240.5485-0.10910.4246-30.7084-17.836937.389
160.3090.184-0.67371.07670.566-0.2408-0.06090.2381-0.1135-0.20520.18780.05080.37330.3499-0.0522-0.0152-0.09250.00610.1088-0.11610.3029-25.5522-13.003733.3143
170.9948-0.425-0.4280.1478-0.00731.42920.02750.0897-0.0347-0.004-0.1412-0.06080.11390.49210.0680.0548-0.0089-0.01180.1205-0.0150.1854-14.597-0.06869.0533
180.23410.2683-0.10230.65780.75320.10660.07260.21540.2346-0.29030.22310.20240.0206-0.0718-0.15050.45-0.22150.01070.4630.04890.5608-33.057-15.500417.5591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 2:23
2X-RAY DIFFRACTION2chain A and resid 24:139
3X-RAY DIFFRACTION3chain A and resid 140:194
4X-RAY DIFFRACTION4chain A and resid 195:240
5X-RAY DIFFRACTION5chain A and resid 241:269
6X-RAY DIFFRACTION6chain A and resid 270:288
7X-RAY DIFFRACTION7chain A and resid 289:323
8X-RAY DIFFRACTION8chain A and resid 324:394
9X-RAY DIFFRACTION9chain A and resid 395:468
10X-RAY DIFFRACTION10chain B and resid 2:23
11X-RAY DIFFRACTION11chain B and resid 24:85
12X-RAY DIFFRACTION12chain B and resid 86:139
13X-RAY DIFFRACTION13chain B and resid 140:193
14X-RAY DIFFRACTION14chain B and resid 194:224
15X-RAY DIFFRACTION15chain B and resid 225:274
16X-RAY DIFFRACTION16chain B and resid 275:323
17X-RAY DIFFRACTION17chain B and resid 324:394
18X-RAY DIFFRACTION18chain B and resid 395:467

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