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- PDB-2f9r: Crystal structure of the inactive state of the Smase I, a sphingo... -

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Basic information

Entry
Database: PDB / ID: 2f9r
TitleCrystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom
ComponentsSphingomyelinase D 1
KeywordsHYDROLASE / sphingomyelinase D / catalytic activity / magnesium-binding site / inactive state
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
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 LlSicTox-alphaIII1i
Similarity search - Component
Biological speciesLoxosceles laeta (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMurakami, M.T. / Gabdoulkhakov, A. / Fernandes-Pedrosa, M.F. / Betzel, C. / Tambourgi, D.V. / Arni, R.K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D.
Authors: Murakami, M.T. / Gabdoulkhakov, A. / Fernandes-Pedrosa, M.F. / Tambourgi, D.V. / Arni, R.K.
History
DepositionDec 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Sphingomyelinase D 1
B: Sphingomyelinase D 1
C: Sphingomyelinase D 1
D: Sphingomyelinase D 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,14411
Polymers128,3324
Non-polymers8127
Water9,134507
1
A: Sphingomyelinase D 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1072
Polymers32,0831
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sphingomyelinase D 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3463
Polymers32,0831
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sphingomyelinase D 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3463
Polymers32,0831
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sphingomyelinase D 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3463
Polymers32,0831
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Sphingomyelinase D 1
D: Sphingomyelinase D 1
hetero molecules

A: Sphingomyelinase D 1
B: Sphingomyelinase D 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,14411
Polymers128,3324
Non-polymers8127
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_664-x+1,-y+1,z-1/21
Buried area9870 Å2
ΔGint-78 kcal/mol
Surface area41600 Å2
MethodPISA
6
A: Sphingomyelinase D 1
B: Sphingomyelinase D 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4535
Polymers64,1662
Non-polymers2873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
C: Sphingomyelinase D 1
D: Sphingomyelinase D 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6916
Polymers64,1662
Non-polymers5254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)140.587, 140.587, 113.608
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe monomer is the biological assembly

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Components

#1: Protein
Sphingomyelinase D 1 / Sphingomyelinase I / SMase I


Mass: 32082.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loxosceles laeta (spider) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8I914, EC: 3.1.4.41
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 11
Details: 2.4 M trisodium citrate, pH 11, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.478 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2005
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.478 Å / Relative weight: 1
ReflectionResolution: 1.85→22.5 Å / Num. all: 90483 / Num. obs: 86016 / % possible obs: 83.47 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 1.85→1.89 Å / % possible all: 83.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code: 1XX1

1xx1


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.783 / SU ML: 0.094 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23398 4467 4.9 %RANDOM
Rwork0.18729 ---
all0.225 90483 --
obs0.18959 86016 83.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.157 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9076 0 49 507 9632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229667
X-RAY DIFFRACTIONr_angle_refined_deg1.341.95213202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2351213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64524.256477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.406151553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2311550
X-RAY DIFFRACTIONr_chiral_restr0.0870.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027556
X-RAY DIFFRACTIONr_nbd_refined0.2170.25801
X-RAY DIFFRACTIONr_nbtor_refined0.3190.26643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2930
X-RAY DIFFRACTIONr_metal_ion_refined0.2170.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.2164
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.234
X-RAY DIFFRACTIONr_mcbond_it1.0381.55858
X-RAY DIFFRACTIONr_mcangle_it1.66129359
X-RAY DIFFRACTIONr_scbond_it2.67434336
X-RAY DIFFRACTIONr_scangle_it3.7354.53810
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 358 -
Rwork0.191 6255 -
obs--83.41 %

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