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- PDB-3g4o: Crystal structure of the activated aerolysin mutant H132N -

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Basic information

Entry
Database: PDB / ID: 3g4o
TitleCrystal structure of the activated aerolysin mutant H132N
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: 2.3 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

Downloads & links

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Assembly

Deposited unit
A: Aerolysin
B: Aerolysin


Theoretical massNumber of molelcules
Total (without water)103,9132
Polymers103,9132
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-4 kcal/mol
Surface area39500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.985, 69.313, 165.230
Angle α, β, γ (deg.)90.00, 109.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aerolysin


Mass: 51956.410 Da / Num. of mol.: 2 / Mutation: H132N
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.: 187 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) 24%-28%, 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: 2.3→55.504 Å / Num. obs: 43658 / % possible obs: 95.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 45.04 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.062 / Net I/σ(I): 16.31
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.69 / Num. unique all: 4969 / Rsym value: 0.311 / % possible all: 74.7

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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: 2.3→55.47 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / Cross valid method: THROUGHOUT / Phase error: 30.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 2186 5.01 %RANDOM
Rwork0.205 ---
obs0.2079 43641 95.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.951 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 170.76 Å2 / Biso mean: 57.34 Å2 / Biso min: 14.46 Å2
Baniso -1Baniso -2Baniso -3
1--10.9134 Å20 Å21.6391 Å2
2--22.1382 Å2-0 Å2
3----16.7369 Å2
Refinement stepCycle: LAST / Resolution: 2.3→55.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6978 0 0 187 7165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057182
X-RAY DIFFRACTIONf_angle_d0.9089799
X-RAY DIFFRACTIONf_chiral_restr0.0631032
X-RAY DIFFRACTIONf_plane_restr0.0041282
X-RAY DIFFRACTIONf_dihedral_angle_d19.2392515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.35010.35881080.2664177666
2.3501-2.40480.32661030.2536210177
2.4048-2.46490.33941420.2523259095
2.4649-2.53150.29691280.2382263098
2.5315-2.6060.35981420.2413266798
2.606-2.69010.28461330.2275270199
2.6901-2.78630.29411610.2145262299
2.7863-2.89780.29291320.2155267099
2.8978-3.02970.29911310.227270599
3.0297-3.18940.26511250.2139270199
3.1894-3.38920.30291380.2154267899
3.3892-3.65090.2551390.2003271099
3.6509-4.01820.2721430.1792271099
4.0182-4.59940.18991530.154271599
4.5994-5.79380.19881620.1552271099
5.7938-55.52030.2011460.1775276998
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)
1-0.01990.0259-0.110.0285-0.0044-0.00580.09030.2053-0.5176-0.0276-0.0118-0.028-0.0385-0.5457-0.00020.26720.03220.03070.2406-0.05620.2321-20.892110.907631.0144
20.1475-0.0161-0.13620.2750.51960.7704-0.0281-0.2877-0.03920.0355-0.0833-0.0748-0.0804-0.22350.00090.16710.09110.03920.29720.03730.2215-19.77642.075733.4639
31.3512-0.1971-0.02130.21170.32030.6246-0.2576-0.0317-0.39010.04840.08390.06220.1627-0.0543-0.06380.2081-0.04670.05330.06790.0250.3692-9.6134-18.835810.6146
40.0045-0.11410.2210.03710.0834-0.08270.4668-0.0745-0.07940.016-0.0143-0.9077-0.74760.0625-0.00011.29760.1237-0.06310.9573-0.04140.49195.266-9.690773.6378
50.2680.41250.12541.39750.26330.5931-0.5336-0.8117-0.12660.06530.8232-0.0165-0.16980.97910.24950.3390.43050.08760.65640.14360.35683.6182-19.025240.681
6-0.61410.4026-0.26390.3023-0.27580.20250.1082-0.1660.01320.41140.23430.29180.5744-0.12520.00170.62460.34640.17060.70220.12260.58250.3905-13.880860.8706
71.3430.2317-0.3597-0.0763-0.30540.0130.0780.0019-0.0421-0.0212-0.1525-0.06650.1171-0.3022-0.00170.18310.0024-0.01740.11440.01810.2703-11.8285-2.31468.7977
80.03240.01320.01670.5993-1.04911.52320.1202-0.2970.1083-0.19770.74460.50920.40270.14090.04960.39210.3830.08390.48070.1630.5124-1.2661-23.535641.3085
9-0.07050.02430.03560.0760.11950.02110.5655-0.37910.11770.0031-0.3122-0.703-0.03750.0954-00.78480.19120.09551.2223-0.01530.75978.2554-15.05671.7888
100.0443-0.1613-0.079-0.0454-0.2702-0.0419-0.0392-0.3156-0.1808-0.01410.38310.2969-0.29190.32030.00120.4142-0.14970.01870.3348-0.06330.2746-6.258114.365243.0855
110.16050.4568-0.05540.33610.09741.0316-0.0476-0.03510.0037-0.02850.0276-0.02330.02250.4209-00.1885-0.05810.00730.3665-0.04110.2385-6.77072.382540.6769
120.14640.08780.2023-0.20240.15710.2432-0.0668-0.099-0.0567-0.1385-0.07940.10610.059-0.01590.00010.38450.0715-0.01350.47370.00030.2481-14.2056-12.957671.735
130.6870.22040.46910.36740.19670.07740.0033-0.1013-0.1209-0.02360.0806-0.15670.17090.158300.43220.0593-0.00790.4183-0.00750.2599-21.2246-14.902761.653
140.69771.06930.03180.4013-0.07310.04750.1005-0.24630.3764-0.15210.22470.3936-0.32440.15900.43890.00860.10110.2286-0.10070.3104-33.5102-15.70484.9672
150.3716-0.0769-0.4340.46660.22040.93080.28111.03530.29810.4191-0.1926-0.2415-0.8358-1.02760.02380.374-0.01850.01020.54390.02430.2771-30.3346-16.292939.0163
160.14690.067-0.1079-0.110.19990.0260.1573-0.190.528-0.28150.08880.2184-0.56420.1067-0.00060.7799-0.21130.10790.3322-0.05960.4167-33.2616-11.49186.575
170.12730.0421-0.25890.15220.04840.41430.0457-0.1198-0.08810.10660.1128-0.06650.0304-0.073600.2887-0.0109-0.04530.3904-0.05770.2264-18.4424-4.545954.9289
180.12420.55630.34830.38890.16280.4679-0.15130.0534-0.0699-0.05560.12290.23-0.3691-0.34810.00230.3374-0.1414-0.00650.2206-0.04660.2808-36.2102-17.48212.0787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 2:17
2X-RAY DIFFRACTION2chain A and resid 18:106
3X-RAY DIFFRACTION3chain A and resid 107:192
4X-RAY DIFFRACTION4chain A and resid 193:224
5X-RAY DIFFRACTION5chain A and resid 225:274
6X-RAY DIFFRACTION6chain A and resid 275:313
7X-RAY DIFFRACTION7chain A and resid 314:395
8X-RAY DIFFRACTION8chain A and resid 396:409
9X-RAY DIFFRACTION9chain A and resid 410:462
10X-RAY DIFFRACTION10chain B and resid 2:23
11X-RAY DIFFRACTION11chain B and resid 24:103
12X-RAY DIFFRACTION12chain B and resid 104:146
13X-RAY DIFFRACTION13chain B and resid 147:193
14X-RAY DIFFRACTION14chain B and resid 194:227
15X-RAY DIFFRACTION15chain B and resid 228:269
16X-RAY DIFFRACTION16chain B and resid 270:289
17X-RAY DIFFRACTION17chain B and resid 290:412
18X-RAY DIFFRACTION18chain B and resid 413:468

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