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- PDB-5fic: Open form of murine Acid Sphingomyelinase in presence of lipid -

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Open data


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Basic information

Entry
Database: PDB / ID: 5fic
TitleOpen form of murine Acid Sphingomyelinase in presence of lipid
ComponentsSphingomyelin phosphodiesterase
KeywordsHYDROLASE / SMPD1 / ASM / ASMase / saposin
Function / homology
Function and homology information


acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / Glycosphingolipid catabolism / lamellar body / sphingomyelin phosphodiesterase activity / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction ...acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / Glycosphingolipid catabolism / lamellar body / sphingomyelin phosphodiesterase activity / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / ceramide biosynthetic process / ceramide metabolic process / plasma membrane repair / response to type I interferon / hydrolase activity, acting on glycosyl bonds / response to ionizing radiation / positive regulation of endocytosis / response to tumor necrosis factor / positive regulation of protein dephosphorylation / cholesterol metabolic process / cellular response to calcium ion / lipid droplet / response to interleukin-1 / response to cocaine / response to virus / wound healing / cellular response to UV / positive regulation of viral entry into host cell / lysosome / endosome / response to xenobiotic stimulus / symbiont entry into host cell / positive regulation of apoptotic process / extracellular space / zinc ion binding / plasma membrane
Similarity search - Function
Sphingomyelin phosphodiesterase / Acid sphingomyelinase/endopolyphosphatase, metallophosphatase domain / Sphingomyelin phosphodiesterase, C-terminal domain / Acid sphingomyelin phosphodiesterase C-terminal region / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
octadecylphosphonic acid / PHOSPHATE ION / Sphingomyelin phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGorelik, A. / Illes, K. / Heinz, L.X. / Superti-Furga, G. / Nagar, B.
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structure of mammalian acid sphingomyelinase.
Authors: Gorelik, A. / Illes, K. / Heinz, L.X. / Superti-Furga, G. / Nagar, B.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Jun 20, 2018Group: Data collection / Derived calculations / Structure summary
Category: pdbx_struct_oper_list / struct_keywords
Item: _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sphingomyelin phosphodiesterase
B: Sphingomyelin phosphodiesterase
C: Sphingomyelin phosphodiesterase
D: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,36634
Polymers241,7274
Non-polymers5,64030
Water70339
1
A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,41011
Polymers60,4321
Non-polymers1,97810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4338
Polymers60,4321
Non-polymers1,0027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3387
Polymers60,4321
Non-polymers9076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1848
Polymers60,4321
Non-polymers1,7537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.750, 101.750, 401.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Sphingomyelin phosphodiesterase / / Acid sphingomyelinase / aSMase


Mass: 60431.633 Da / Num. of mol.: 4 / Fragment: UNP residues 84-611
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smpd1, Asm / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04519, sphingomyelin phosphodiesterase

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Sugars , 4 types, 8 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 61 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-6E0 / octadecylphosphonic acid / Octadecylphosphonic acid


Mass: 334.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H39O3P
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 4.3 Å3/Da / Density % sol: 71.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium/potassium phosphate, MES, sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97959 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.8→49.318 Å / Num. obs: 99971 / % possible obs: 100 % / Redundancy: 6.725 % / Net I/σ(I): 9.92

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HNQ

5hnq


Resolution: 2.8→49.318 Å / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 23.76 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2356 968 0.97 %
Rwork0.1891 --
obs0.1912 99739 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16640 0 330 39 17009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517610
X-RAY DIFFRACTIONf_angle_d0.6424102
X-RAY DIFFRACTIONf_dihedral_angle_d11.80410364
X-RAY DIFFRACTIONf_chiral_restr0.0392586
X-RAY DIFFRACTIONf_plane_restr0.0043086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.94780.31491360.248714087X-RAY DIFFRACTION99
2.9478-3.13240.30041380.226614059X-RAY DIFFRACTION99
3.1324-3.3740.30881380.20714087X-RAY DIFFRACTION99
3.374-3.71320.22461360.196314096X-RAY DIFFRACTION99
3.7132-4.24960.25431420.175614121X-RAY DIFFRACTION99
4.2496-5.35070.20641370.160814115X-RAY DIFFRACTION99
5.3507-33.91910.19851410.186114148X-RAY DIFFRACTION99

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