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- PDB-9ozs: Structure of phospholipase D BetaIB1i from Sicarius terrosus veno... -

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Basic information

Entry
Database: PDB / ID: 9ozs
TitleStructure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to substrate sphingolipids at 2.60 A resolution
ComponentsDermonecrotic toxin StSicTox-betaIB1i
KeywordsLYASE / toxin sphingolipid spider venom interfacial binding site
Function / homology
Function and homology information


phosphoric diester hydrolase activity / lipid catabolic process / toxin activity / Lyases; Phosphorus-oxygen lyases / killing of cells of another organism / lyase activity / extracellular region / metal ion binding
Similarity search - Function
Glycerophosphoryl diester phosphodiesterase family / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
Similarity search - Domain/homology
: / Dermonecrotic toxin StSicTox-betaIB1i
Similarity search - Component
Biological speciesSicarius terrosus (spider)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSundman, A.K. / Montfort, W.R. / Binford, G.J. / Cordes, M.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1808716 United States
CitationJournal: To Be Published
Title: Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 1.85 A resolution
Authors: Sundman, A.K. / Montfort, W.R. / Binford, G.J. / Cordes, M.H.
History
DepositionJun 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dermonecrotic toxin StSicTox-betaIB1i
B: Dermonecrotic toxin StSicTox-betaIB1i
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,40014
Polymers68,5252
Non-polymers3,87612
Water12,376687
1
A: Dermonecrotic toxin StSicTox-betaIB1i
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3188
Polymers34,2621
Non-polymers2,0567
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dermonecrotic toxin StSicTox-betaIB1i
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0826
Polymers34,2621
Non-polymers1,8205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.789, 105.854, 109.108
Angle α, β, γ (deg.)90.00, 93.62, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-515-

HOH

21B-751-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dermonecrotic toxin StSicTox-betaIB1i / Phospholipase D / PLD / Sphingomyelin phosphodiesterase D / SMD / SMase D / Sphingomyelinase D


Mass: 34262.332 Da / Num. of mol.: 2 / Mutation: H47N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sicarius terrosus (spider) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D4WV12, Lyases; Phosphorus-oxygen lyases

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Non-polymers , 5 types, 699 molecules

#2: Chemical
ChemComp-A1A43 / 2-aminoethyl (2S,3R,4E)-2-dodecanamido-3-hydroxyheptadec-4-en-1-yl hydrogen (S)-phosphate


Mass: 590.815 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H63N2O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1 mg/mL protein, 0.4 mM ceramidephosphoethanolamine, 5 mg/mL CHAPS, 8.25% methyl-2,4-pentanediol, 75 mM sodium chloride, 27.5 mM sodium acetate (pH 4.6), ~30 mM Tris, 1 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Dec 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.6→24.41 Å / Num. obs: 28219 / % possible obs: 99.8 % / Redundancy: 9 % / CC1/2: 0.941 / Rmerge(I) obs: 0.4 / Net I/σ(I): 4.1
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 7 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3441 / CC1/2: 0.49 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
PROTEUM2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→24.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.797 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20889 1528 5.4 %RANDOM
Rwork0.14906 ---
obs0.15231 26690 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.505 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.2 Å2
2--0.12 Å20 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 2.6→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 260 687 5423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124825
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164644
X-RAY DIFFRACTIONr_angle_refined_deg1.781.8656476
X-RAY DIFFRACTIONr_angle_other_deg0.5961.78510719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6215556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.011554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96210795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021136
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4711.672227
X-RAY DIFFRACTIONr_mcbond_other1.4661.672227
X-RAY DIFFRACTIONr_mcangle_it2.432.9962782
X-RAY DIFFRACTIONr_mcangle_other2.4322.9972783
X-RAY DIFFRACTIONr_scbond_it3.1282.3852598
X-RAY DIFFRACTIONr_scbond_other3.1282.3872599
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.214.0993695
X-RAY DIFFRACTIONr_long_range_B_refined7.12917.945726
X-RAY DIFFRACTIONr_long_range_B_other7.03517.885635
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 98 -
Rwork0.255 1964 -
obs--99.95 %

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