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- PDB-4q6x: Structure of phospholipase D Beta1B1i from Sicarius terrosus veno... -

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Basic information

Entry
Database: PDB / ID: 4q6x
TitleStructure of phospholipase D Beta1B1i from Sicarius terrosus venom at 2.14 A resolution
ComponentsPhospholipase D StSicTox-betaIC1
KeywordsLYASE / TIM Barrel / Venom gland secretion of Sicarius terrosus
Function / homology
Function and homology information


phosphoric diester hydrolase activity / lipid catabolic process / Lyases; Phosphorus-oxygen lyases / toxin activity / killing of cells of another organism / lyase activity / extracellular region / metal ion binding
Similarity search - Function
Glycerophosphoryl diester phosphodiesterase family / Phosphatidylinositol (PI) phosphodiesterase / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Dermonecrotic toxin StSicTox-betaIB1i
Similarity search - Component
Biological speciesSicarius terrosus (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsLajoie, D.M. / Roberts, S.A. / Zobel-Thropp, P.A. / Binford, G.J. / Cordes, M.H.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Variable Substrate Preference among Phospholipase D Toxins from Sicariid Spiders.
Authors: Lajoie, D.M. / Roberts, S.A. / Zobel-Thropp, P.A. / Delahaye, J.L. / Bandarian, V. / Binford, G.J. / Cordes, M.H.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase D StSicTox-betaIC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3112
Polymers34,2861
Non-polymers241
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.222, 49.222, 90.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Phospholipase D StSicTox-betaIC1 / PLD / Dermonecrotic toxin / Sphingomyelin phosphodiesterase D / SMD / SMase D / Sphingomyelinase D


Mass: 34286.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sicarius terrosus (spider) / Gene: StSicTox-betaIC1i / Plasmid: pHis8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0D4WV12*PLUS, cyclic pyranopterin monophosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
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: 1.84 Å3/Da / Density % sol: 33.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3 mg/ml protein, 12% PEG 3350, 0.1M Bis-Tris, 0.1M magnesium chloride , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2013
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.14→38.56 Å / Num. all: 13352 / Num. obs: 13352 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.9
Reflection shellResolution: 2.14→2.25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1828 / % possible all: 94.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RLH

3rlh


Resolution: 2.14→38.56 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.06 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.307 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22069 651 4.9 %RANDOM
Rwork0.16415 ---
all0.16689 13325 --
obs0.16689 12674 99.14 %-
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: 39.122 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.34 Å2-0 Å2
2--0.34 Å20 Å2
3----1.12 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.14→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 1 122 2363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192289
X-RAY DIFFRACTIONr_bond_other_d0.0010.022134
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9563097
X-RAY DIFFRACTIONr_angle_other_deg0.7663.0024900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6925277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93623.448116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83715397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9331521
X-RAY DIFFRACTIONr_chiral_restr0.0780.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
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_it1.6792.8211111
X-RAY DIFFRACTIONr_mcbond_other1.6792.8211110
X-RAY DIFFRACTIONr_mcangle_it2.5474.2271387
X-RAY DIFFRACTIONr_mcangle_other2.5464.2271388
X-RAY DIFFRACTIONr_scbond_it1.9643.0271178
X-RAY DIFFRACTIONr_scbond_other1.9643.0271178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1424.4491710
X-RAY DIFFRACTIONr_long_range_B_refined4.45422.7612732
X-RAY DIFFRACTIONr_long_range_B_other4.41622.722711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.139→2.194 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 47 -
Rwork0.212 795 -
obs--91.22 %
Refinement TLS params.Method: refined / Origin x: -8.075 Å / Origin y: 42 Å / Origin z: 0.646 Å
111213212223313233
T0.0733 Å20.0625 Å2-0.0003 Å2-0.0594 Å2-0.0022 Å2--0.0272 Å2
L1.4395 °2-0.2176 °2-0.3139 °2-0.966 °2-0.0401 °2--0.7754 °2
S0.0827 Å °0.0202 Å °-0.0117 Å °-0.0707 Å °-0.0298 Å °0.0033 Å °-0.0228 Å °-0.0505 Å °-0.053 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A401 - 522
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A1 - 278

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