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- PDB-5fi9: Closed form of murine Acid Sphingomyelinase in complex with bisph... -

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Basic information

Entry
Database: PDB / ID: 5fi9
TitleClosed form of murine Acid Sphingomyelinase in complex with bisphosphonate inhibitor AbPA
ComponentsSphingomyelin phosphodiesterase
KeywordsHYDROLASE / SMPD1 / ASM / ASMase / saposin
Function / homology
Function and homology information


acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / lamellar body / Glycosphingolipid catabolism / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / ceramide metabolic process ...acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / lamellar body / Glycosphingolipid catabolism / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / ceramide metabolic process / plasma membrane repair / ceramide biosynthetic process / response to type I interferon / hydrolase activity, acting on glycosyl bonds / response to ionizing radiation / positive regulation of endocytosis / response to tumor necrosis factor / : / cholesterol metabolic process / response to interleukin-1 / cellular response to calcium ion / lipid droplet / response to cocaine / wound healing / response to virus / cellular response to UV / lysosome / positive regulation of viral entry into host cell / positive regulation of apoptotic process / symbiont entry into host cell / response to xenobiotic stimulus / 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
(1-azanyl-1-phosphono-decyl)phosphonic acid / Sphingomyelin phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.543 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 1.3May 22, 2019Group: Data collection / Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
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_validate_close_contact / struct_asym / struct_conn / 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 / _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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,28317
Polymers120,8632
Non-polymers6,41915
Water97354
1
A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7809
Polymers60,4321
Non-polymers3,3498
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5028
Polymers60,4321
Non-polymers3,0717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.394, 72.018, 74.420
Angle α, β, γ (deg.)80.47, 71.52, 83.60
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sphingomyelin phosphodiesterase / Acid sphingomyelinase / aSMase


Mass: 60431.633 Da / Num. of mol.: 2 / 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 , 5 types, 9 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.: 4
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.: 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 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 60 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-NT8 / (1-azanyl-1-phosphono-decyl)phosphonic acid


Mass: 317.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H25NO6P2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: lithium acetate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.28154 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28154 Å / Relative weight: 1
ReflectionResolution: 2.543→46.654 Å / Num. obs: 35624 / % possible obs: 97.2 % / Redundancy: 2.9 % / Net I/σ(I): 9.68

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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: 2.543→46.654 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.77 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1681 5 %
Rwork0.2006 --
obs0.2032 33629 91.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.543→46.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8294 0 410 54 8758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049042
X-RAY DIFFRACTIONf_angle_d0.72712407
X-RAY DIFFRACTIONf_dihedral_angle_d11.8525331
X-RAY DIFFRACTIONf_chiral_restr0.0441393
X-RAY DIFFRACTIONf_plane_restr0.0041551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5433-2.61810.3156880.25661669X-RAY DIFFRACTION57
2.6181-2.70260.34861130.25032138X-RAY DIFFRACTION75
2.7026-2.79920.3331360.25342593X-RAY DIFFRACTION90
2.7992-2.91130.30291480.24672824X-RAY DIFFRACTION97
2.9113-3.04370.32051490.25292816X-RAY DIFFRACTION97
3.0437-3.20420.29341490.23812848X-RAY DIFFRACTION98
3.2042-3.40490.2931510.2212847X-RAY DIFFRACTION98
3.4049-3.66770.29781470.21272811X-RAY DIFFRACTION98
3.6677-4.03660.24171500.18532847X-RAY DIFFRACTION98
4.0366-4.62020.20661510.16282860X-RAY DIFFRACTION98
4.6202-5.81920.1961490.16022838X-RAY DIFFRACTION99
5.8192-46.66160.19251500.17812857X-RAY DIFFRACTION98

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