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- PDB-3rlg: Crystal structure of Loxosceles intermedia phospholipase D isofor... -

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Basic information

Entry
Database: PDB / ID: 3rlg
TitleCrystal structure of Loxosceles intermedia phospholipase D isoform 1 H12A mutant
ComponentsSphingomyelin phosphodiesterase D LiSicTox-alphaIA1a
KeywordsHYDROLASE / TIM beta/alpha-barrel / PLC-like phosphodiesterase / inactive mutant H12A phospholipase D
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Dermonecrotic toxin LiSicTox-alphaIA1a
Similarity search - Component
Biological speciesLoxosceles intermedia (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsGiuseppe, P.O. / Ullah, A. / Veiga, S.S. / Murakami, M.T. / Arni, R.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and preliminary X-ray diffraction analysis of a class II phospholipase D from Loxosceles intermedia venom.
Authors: Ullah, A. / de Giuseppe, P.O. / Murakami, M.T. / Trevisan-Silva, D. / Wille, A.C. / Chaves-Moreira, D. / Gremski, L.H. / da Silveira, R.B. / Sennf-Ribeiro, A. / Chaim, O.M. / Veiga, S.S. / Arni, R.K.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingomyelin phosphodiesterase D LiSicTox-alphaIA1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,45810
Polymers33,6731
Non-polymers7859
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.575, 49.455, 56.395
Angle α, β, γ (deg.)90.00, 105.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sphingomyelin phosphodiesterase D LiSicTox-alphaIA1a / Dermonecrotic protein 1 / LiRecDT1 / Sphingomyelin phosphodiesterase D 1 / SMD 1 / SMase D 1 / ...Dermonecrotic protein 1 / LiRecDT1 / Sphingomyelin phosphodiesterase D 1 / SMD 1 / SMase D 1 / Sphingomyelinase D 1


Mass: 33672.625 Da / Num. of mol.: 1 / Mutation: H12A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loxosceles intermedia (spider) / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0CE80, EC: 3.1.4.41

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Non-polymers , 5 types, 247 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris-HCl pH 7.5 and 35%(v/v) PEG200 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 34632 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.663.30.37192.4
1.66-1.724.20.356199.2
1.72-1.85.10.288199.9
1.8-1.95.40.2161100
1.9-2.025.40.1621100
2.02-2.175.40.131100
2.17-2.395.40.1171100
2.39-2.745.50.0911100
2.74-3.455.60.0631100
3.45-305.30.053197.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RLH

3rlh


Resolution: 1.6→27.16 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.61 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19791 1730 5 %RANDOM
Rwork0.16428 ---
obs0.16601 32820 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.04 Å2
2--0.16 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 51 238 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.9463123
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17724.831118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13615363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2581513
X-RAY DIFFRACTIONr_chiral_restr0.1660.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211785
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3821.51395
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17522243
X-RAY DIFFRACTIONr_scbond_it3.2263914
X-RAY DIFFRACTIONr_scangle_it4.844.5872
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 105 -
Rwork0.402 2042 -
obs--84.83 %

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