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- PDB-5kas: Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B) ... -

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Basic information

Entry
Database: PDB / ID: 5kas
TitleMurine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B) with phosphocholine
ComponentsAcid sphingomyelinase-like phosphodiesterase 3b
KeywordsHYDROLASE / phosphoesterase / extracellular / membrane / phosphocholine
Function / homology
Function and homology information


membrane lipid catabolic process / sphingomyelin catabolic process / sphingomyelin phosphodiesterase activity / negative regulation of toll-like receptor signaling pathway / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / hydrolase activity, acting on glycosyl bonds / negative regulation of innate immune response / negative regulation of inflammatory response / inflammatory response ...membrane lipid catabolic process / sphingomyelin catabolic process / sphingomyelin phosphodiesterase activity / negative regulation of toll-like receptor signaling pathway / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / hydrolase activity, acting on glycosyl bonds / negative regulation of innate immune response / negative regulation of inflammatory response / inflammatory response / innate immune response / extracellular space / zinc ion binding / plasma membrane
Similarity search - Function
Acid sphingomyelinase-like phosphodiesterase, predicted / Acid sphingomyelinase/endopolyphosphatase, metallophosphatase domain / Sphingomyelin phosphodiesterase, C-terminal domain / Acid sphingomyelin phosphodiesterase C-terminal region / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
NITRATE ION / PHOSPHOCHOLINE / Acid sphingomyelinase-like phosphodiesterase 3b
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.619 Å
AuthorsGorelik, A. / Illes, K. / Heinz, L.X. / Superti-Furga, G. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity.
Authors: Gorelik, A. / Heinz, L.X. / Illes, K. / Superti-Furga, G. / Nagar, B.
History
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Data collection / Database references
Category: chem_comp / citation / pdbx_audit_support
Item: _chem_comp.type / _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
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_special_symmetry / 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_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.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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.ptnr2_symmetry / _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: Acid sphingomyelinase-like phosphodiesterase 3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,19312
Polymers48,8151
Non-polymers2,37911
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.892, 47.031, 93.861
Angle α, β, γ (deg.)90.00, 98.07, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-504-

ZN

21A-722-

HOH

31A-807-

HOH

41A-908-

HOH

51A-948-

HOH

61A-986-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acid sphingomyelinase-like phosphodiesterase 3b / ASM-like phosphodiesterase 3b


Mass: 48814.629 Da / Num. of mol.: 1 / Fragment: UNP residues 19-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smpdl3b, Asml3b / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P58242, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Sugars , 3 types, 3 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.: 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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 1
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

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Non-polymers , 4 types, 411 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-PC / PHOSPHOCHOLINE


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


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.619→31.993 Å / Num. obs: 50664 / % possible obs: 90.5 % / Redundancy: 6.7 % / Net I/σ(I): 12.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.619→31.993 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.49
RfactorNum. reflection% reflection
Rfree0.1928 2536 5.04 %
Rwork0.1692 --
obs0.1704 50344 89.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.619→31.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 140 403 3863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053597
X-RAY DIFFRACTIONf_angle_d0.7924934
X-RAY DIFFRACTIONf_dihedral_angle_d10.4942108
X-RAY DIFFRACTIONf_chiral_restr0.045544
X-RAY DIFFRACTIONf_plane_restr0.005631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6189-1.650.2479610.23141215X-RAY DIFFRACTION41
1.65-1.68370.2743900.22891678X-RAY DIFFRACTION57
1.6837-1.72030.25831110.22681894X-RAY DIFFRACTION65
1.7203-1.76030.24951190.21772207X-RAY DIFFRACTION75
1.7603-1.80430.26031440.21882634X-RAY DIFFRACTION89
1.8043-1.85310.26121530.20632881X-RAY DIFFRACTION98
1.8531-1.90760.30511410.28632853X-RAY DIFFRACTION95
1.9076-1.96920.2881590.27952885X-RAY DIFFRACTION98
1.9692-2.03960.18221620.16622956X-RAY DIFFRACTION99
2.0396-2.12120.19531430.15792904X-RAY DIFFRACTION99
2.1212-2.21770.2111450.19282897X-RAY DIFFRACTION97
2.2177-2.33460.26481310.22462882X-RAY DIFFRACTION97
2.3346-2.48080.19421790.152937X-RAY DIFFRACTION99
2.4808-2.67230.14771370.1462989X-RAY DIFFRACTION100
2.6723-2.9410.17641620.15622959X-RAY DIFFRACTION100
2.941-3.36620.18491660.15242982X-RAY DIFFRACTION100
3.3662-4.23950.15181820.13722980X-RAY DIFFRACTION100
4.2395-31.99970.1721510.14843075X-RAY DIFFRACTION99

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