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- PDB-5hqn: Catalytic domain of murine Acid Sphingomyelinase (ASMase, ASM, SMPD1) -

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Basic information

Entry
Database: PDB / ID: 5hqn
TitleCatalytic domain of murine Acid Sphingomyelinase (ASMase, ASM, SMPD1)
ComponentsSphingomyelin phosphodiesterase
KeywordsHYDROLASE / SMPD1 / ASM / ASMase / sphingomyelinase / HYDROLASE-HYDROLASE Inhibitor complex
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
PHOSPHATE ION / Sphingomyelin phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionJan 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_oper_list / pdbx_validate_close_contact / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,93915
Polymers107,2812
Non-polymers3,65813
Water1,33374
1
A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2867
Polymers53,6411
Non-polymers1,6456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6538
Polymers53,6411
Non-polymers2,0127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.844, 127.297, 102.523
Angle α, β, γ (deg.)90.00, 121.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 53640.613 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 165-627)
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 , 3 types, 7 molecules

#2: 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.: 3
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
#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.: 3
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
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 3 types, 80 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: sodium phosphate, potassium phosphate, MES, sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 52772 / % possible obs: 99.6 % / Redundancy: 6.8 % / Net I/σ(I): 6.68

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.864 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 1589 3.79 %
Rwork0.2126 --
obs0.2144 41925 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→38.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7050 0 226 74 7350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057572
X-RAY DIFFRACTIONf_angle_d0.66910385
X-RAY DIFFRACTIONf_dihedral_angle_d10.654405
X-RAY DIFFRACTIONf_chiral_restr0.0421114
X-RAY DIFFRACTIONf_plane_restr0.0041330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68390.36041440.31273642X-RAY DIFFRACTION100
2.6839-2.77980.31471440.29463670X-RAY DIFFRACTION100
2.7798-2.89110.31591420.2743628X-RAY DIFFRACTION100
2.8911-3.02260.31921450.27053657X-RAY DIFFRACTION100
3.0226-3.18190.32671460.26123693X-RAY DIFFRACTION100
3.1819-3.38110.29271420.24393617X-RAY DIFFRACTION100
3.3811-3.6420.27851440.21333669X-RAY DIFFRACTION100
3.642-4.00820.24891450.1943672X-RAY DIFFRACTION100
4.0082-4.58740.22291450.17673661X-RAY DIFFRACTION100
4.5874-5.77660.19891440.17263681X-RAY DIFFRACTION100
5.7766-38.86880.23011480.19333746X-RAY DIFFRACTION100

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