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- PDB-3cqf: Crystal structure of anthrolysin O (ALO) -

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Basic information

Entry
Database: PDB / ID: 3cqf
TitleCrystal structure of anthrolysin O (ALO)
ComponentsThiol-activated cytolysin
KeywordsTOXIN / Anthrolysin O / cytolysin / Anthrax
Function / homology
Function and homology information


hemolysis in another organism / cholesterol binding / : / toxin activity / membrane => GO:0016020 / host cell plasma membrane / extracellular region
Similarity search - Function
Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain ...Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Glutaredoxin / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Anthrolysin O/cereolysin O family cholesterol-dependent cytolysin / Thiol-activated cytolysin
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsBourdeau, R.W. / Malito, E. / Tang, W.J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Cellular Functions and X-ray Structure of Anthrolysin O, a Cholesterol-dependent Cytolysin Secreted by Bacillus anthracis
Authors: Bourdeau, R.W. / Malito, E. / Chenal, A. / Bishop, B.L. / Musch, M.W. / Villereal, M.L. / Chang, E.B. / Mosser, E.M. / Rest, R.F. / Tang, W.J.
History
DepositionApr 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol-activated cytolysin
B: Thiol-activated cytolysin


Theoretical massNumber of molelcules
Total (without water)108,1292
Polymers108,1292
Non-polymers00
Water48627
1
A: Thiol-activated cytolysin


Theoretical massNumber of molelcules
Total (without water)54,0641
Polymers54,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol-activated cytolysin


Theoretical massNumber of molelcules
Total (without water)54,0641
Polymers54,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.740, 141.749, 294.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTYRTYRAA46 - 40223 - 379
21LYSLYSTYRTYRBB46 - 40223 - 379
32SERSERHISHISAA403 - 512380 - 489
42SERSERHISHISBB403 - 512380 - 489

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Components

#1: Protein Thiol-activated cytolysin


Mass: 54064.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Plasmid: pProEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81N62, UniProt: A0A6L7HHW7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5M Sodium formate, 0.1M Hepes, 0.01M Taurine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 53120 / Num. obs: 52355 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.1→3.21 Å / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0067refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PFO

1pfo


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.863 / SU B: 15.84 / SU ML: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.486 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2624 5 %RANDOM
Rwork0.268 ---
all0.27 53120 --
obs0.27 50234 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 76.769 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7074 0 0 27 7101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227216
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9399848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4975920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15825.759316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.652151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9931520
X-RAY DIFFRACTIONr_chiral_restr0.0940.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215460
X-RAY DIFFRACTIONr_mcbond_it0.7311.54618
X-RAY DIFFRACTIONr_mcangle_it1.37927482
X-RAY DIFFRACTIONr_scbond_it1.43632598
X-RAY DIFFRACTIONr_scangle_it2.5794.52366
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3537 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.010.05
TIGHT THERMAL0.020.5
LS refinement shellResolution: 3.1→3.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 164 -
Rwork0.377 3539 -
all-3703 -
obs--95.88 %

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