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- PDB-4wvm: Stonustoxin structure -

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Basic information

Entry
Database: PDB / ID: 4wvm
TitleStonustoxin structure
Components
  • Stonustoxin subunit alpha
  • Stonustoxin subunit beta
KeywordsTOXIN / MACPF CDC / Membrane Attack Complex / Perforin Cholesterol Dependent / Cytolysin / Venom / PRY / SPRY / Thioredoxin Focal adhesion targeting
Function / homology
Function and homology information


hemolysis in another organism / toxin activity / extracellular region
Similarity search - Function
SNTX, thioredoxin-like domain / Thioredoxin-like SNTX domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. ...SNTX, thioredoxin-like domain / Thioredoxin-like SNTX domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Stonustoxin subunit beta / Stonustoxin subunit alpha
Similarity search - Component
Biological speciesSynanceia horrida (estuarine stonefish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å
AuthorsEllisdon, A.M. / Panjikar, S. / Whisstock, J.C. / McGowan, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Stonefish toxin defines an ancient branch of the perforin-like superfamily.
Authors: Ellisdon, A.M. / Reboul, C.F. / Panjikar, S. / Huynh, K. / Oellig, C.A. / Winter, K.L. / Dunstone, M.A. / Hodgson, W.C. / Seymour, J. / Dearden, P.K. / Tweten, R.K. / Whisstock, J.C. / McGowan, S.
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stonustoxin subunit alpha
B: Stonustoxin subunit beta


Theoretical massNumber of molelcules
Total (without water)159,1392
Polymers159,1392
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-5 kcal/mol
Surface area54040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.911, 107.911, 244.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Stonustoxin subunit alpha / SNTX subunit alpha


Mass: 79623.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synanceia horrida (estuarine stonefish) / References: UniProt: Q98989
#2: Protein Stonustoxin subunit beta / SNTX subunit beta


Mass: 79516.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synanceia horrida (estuarine stonefish) / References: UniProt: Q91453

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 4.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95659 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95659 Å / Relative weight: 1
ReflectionResolution: 3.1→38.15 Å / Num. all: 50333 / Num. obs: 50233 / % possible obs: 99.1 % / Redundancy: 4.59 % / Biso Wilson estimate: 33.47 Å2 / Net I/σ(I): 11.72

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
Cootmodel building
XSCALEdata scaling
SHELXDEphasing
XDSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.1→38.15 Å / Cor.coef. Fo:Fc: 0.8648 / Cor.coef. Fo:Fc free: 0.8319 / SU R Cruickshank DPI: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.511 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.322
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 2549 5.07 %RANDOM
Rwork0.2071 ---
obs0.2086 50233 99.59 %-
Displacement parametersBiso mean: 48.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2---1.59 Å20 Å2
3---3.1801 Å2
Refine analyzeLuzzati coordinate error obs: 0.604 Å
Refinement stepCycle: 1 / Resolution: 3.1→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9691 0 0 0 9691
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019892HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1213367HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4559SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes246HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1407HARMONIC5
X-RAY DIFFRACTIONt_it9892HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion3.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1299SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11024SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2731 174 4.69 %
Rwork0.2472 3533 -
all0.2484 3707 -
obs--99.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.10770.1758-1.77362.7076-0.4534.6603-0.0594-0.0007-0.3083-0.1112-0.15540.27770.2831-0.63810.21480.0219-0.15650.1310.4096-0.15080.30313.297136.172311.6124
20.82330.1198-0.75191.1531-0.49942.1305-0.09390.3943-0.2386-0.2808-0.06920.23380.1747-0.5670.1631-0.00440.18-0.0748-0.05950.0247-0.247534.675352.8075-27.5967
34.6396-0.2359-1.94164.6678-0.54424.9805-0.066-0.1924-0.2290.0275-0.1326-0.03560.1437-0.04320.1987-0.1816-0.11210.2280.5413-0.01330.2148-1.301244.883933.257
40.96630.3189-1.01861.5861-1.71692.92730.1036-0.3590.06240.101-0.13250.1937-0.3161-0.2110.02890.12920.0527-0.0292-0.13670.0575-0.230439.028262.04252.7572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|4 - 248 }
2X-RAY DIFFRACTION2{ B|264 - 698 }
3X-RAY DIFFRACTION3{ A|4 - 249 }
4X-RAY DIFFRACTION4{ A|266 - 701 }

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