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- PDB-5i85: aSMase with zinc and phosphocholine -

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Basic information

Entry
Database: PDB / ID: 5i85
TitleaSMase with zinc and phosphocholine
ComponentsSphingomyelin phosphodiesterase
KeywordsHYDROLASE / acid sphingomyelinase / phosphocholine
Function / homology
Function and homology information


acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / lamellar body / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction ...acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / lamellar body / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / glycosphingolipid catabolic process / ceramide biosynthetic process / plasma membrane repair / Glycosphingolipid catabolism / hydrolase activity, acting on glycosyl bonds / response to type I interferon / response to ionizing radiation / positive regulation of endocytosis / response to tumor necrosis factor / positive regulation of protein dephosphorylation / cellular response to calcium ion / cholesterol metabolic process / response to interleukin-1 / lysosomal lumen / lipid droplet / negative regulation of MAP kinase activity / response to cocaine / wound healing / response to virus / cellular response to UV / nervous system development / positive regulation of viral entry into host cell / lysosome / endosome / response to xenobiotic stimulus / symbiont entry into host cell / positive regulation of apoptotic process / signal transduction / extracellular space / zinc ion binding / extracellular exosome / 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
PHOSPHOCHOLINE / Sphingomyelin phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsZhou, Y.F. / Wei, R.R.
CitationJournal: Nat Commun / Year: 2016
Title: Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease.
Authors: Zhou, Y.F. / Metcalf, M.C. / Garman, S.C. / Edmunds, T. / Qiu, H. / Wei, R.R.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 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_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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.occupancy / _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 / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _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
Revision 2.1Mar 24, 2021Group: Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity_src_gen / struct_conn
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,07121
Polymers65,1141
Non-polymers3,95720
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sphingomyelin phosphodiesterase
hetero molecules

A: Sphingomyelin phosphodiesterase
hetero molecules

A: Sphingomyelin phosphodiesterase
hetero molecules

A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,28584
Polymers260,4574
Non-polymers15,82880
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_554x,x-y,-z-1/31
Buried area25600 Å2
ΔGint-658 kcal/mol
Surface area89120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.601, 131.601, 188.573
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-950-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sphingomyelin phosphodiesterase / Acid sphingomyelinase / aSMase


Mass: 65114.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMPD1, ASM / Plasmid: pIRES2 / Cell line (production host): HEK293S Gnt1- / Production host: Homo sapiens (human)
References: UniProt: P17405, sphingomyelin phosphodiesterase

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Sugars , 4 types, 6 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}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.: 1
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
#5: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 4 types, 275 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 3.62 Å3/Da / Density % sol: 66.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: phosphocholine soaked in well solution containing 1.5 M ammonium sulfate, 0.1 M sodium acetate pH 5.0-5.5, 12% glycerol.
PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→48.7 Å / Num. obs: 34056 / % possible obs: 99.9 % / Redundancy: 17.3 % / Biso Wilson estimate: 30.76 Å2 / Rsym value: 0.2 / Net I/av σ(I): 3.476 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.6413.90.8220.91100
2.64-2.814.50.6621.11100
2.8-2.9915.70.51.51100
2.99-3.2317.20.3362.21100
3.23-3.5418.50.2343.11100
3.54-3.9519.40.17541100
3.95-4.5620.10.1374.91100
4.56-5.5920.50.1125.91100
5.59-7.9120.40.0927.51100
7.91-31.17518.50.0415.6198.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.63 Å31.17 Å
Translation2.63 Å31.17 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2229: ???)refinement
CrystalCleardata collection
SCALA3.3.21data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I81

5i81


Resolution: 2.5→31.175 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1676 4.93 %
Rwork0.1903 --
obs0.1919 33985 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→31.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 238 261 4660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184557
X-RAY DIFFRACTIONf_angle_d0.8856235
X-RAY DIFFRACTIONf_dihedral_angle_d14.0432642
X-RAY DIFFRACTIONf_chiral_restr0.048682
X-RAY DIFFRACTIONf_plane_restr0.007782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57360.32021510.25472625X-RAY DIFFRACTION100
2.5736-2.65660.29311430.23842625X-RAY DIFFRACTION100
2.6566-2.75150.24891370.23442642X-RAY DIFFRACTION100
2.7515-2.86160.25861250.22282674X-RAY DIFFRACTION100
2.8616-2.99170.27921400.22942650X-RAY DIFFRACTION100
2.9917-3.14930.26521410.21972653X-RAY DIFFRACTION100
3.1493-3.34640.25621360.20672657X-RAY DIFFRACTION100
3.3464-3.60440.23931370.19482677X-RAY DIFFRACTION100
3.6044-3.96650.19131300.17392705X-RAY DIFFRACTION100
3.9665-4.5390.15211320.14622726X-RAY DIFFRACTION100
4.539-5.71290.18971560.15452753X-RAY DIFFRACTION100
5.7129-31.1770.18761480.17512922X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9436-0.17470.69866.9250.48471.66440.01650.15040.2727-0.2940.0290.53230.1801-0.093-0.13920.2714-0.21930.00960.56-0.00310.3559-32.0149-53.4368-43.2966
21.01570.1910.60050.63790.2011.229-0.13070.36490.0575-0.2050.110.04690.02720.09460.0110.2229-0.1387-0.0230.39570.04280.2132-8.4684-36.5066-33.4933
31.63370.33030.51821.29260.05872.1811-0.04420.4509-0.1991-0.21810.1475-0.0160.36240.1879-0.09660.2329-0.065-0.00140.3174-0.07030.2326-0.99-49.753-31.9245
40.9744-0.34850.63010.91910.06221.991-0.07070.2195-0.01590.01320.15950.02980.1940.1122-0.06150.1315-0.0674-0.00690.24170.01160.1785-2.6569-41.1269-17.0606
51.3917-0.04440.11412.0621-1.10562.2558-0.1570.07560.20770.07280.19410.116-0.2219-0.0858-0.00330.149-0.0412-0.04880.22150.00990.1885-8.1869-27.2748-13.2717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 127 )
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 324 )
3X-RAY DIFFRACTION3chain 'A' and (resid 325 through 416 )
4X-RAY DIFFRACTION4chain 'A' and (resid 417 through 510 )
5X-RAY DIFFRACTION5chain 'A' and (resid 511 through 611 )

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