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- PDB-5ebb: Structure of human sphingomyelinase phosphodiesterase like 3A (SM... -

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Basic information

Entry
Database: PDB / ID: 5ebb
TitleStructure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with Zn2+
ComponentsAcid sphingomyelinase-like phosphodiesterase 3a
KeywordsHYDROLASE / calcineurin like phosphodiesterase / binuclear metallophosphodiesterase / acid sphingomyelinase like
Function / homology
Function and homology information


nucleoside triphosphate catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / extracellular space / zinc ion binding / extracellular exosome
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
MALONATE ION / Acid sphingomyelinase-like phosphodiesterase 3a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLim, S.M. / Yeung, K. / Tresaugues, L. / Teo, H.L. / Nordlund, P.
Funding support Singapore, Sweden, 2items
OrganizationGrant numberCountry
National Research FoundationNRF-CRP4-2008-02 Singapore
Swedish Cancer Society Sweden
CitationJournal: Febs J. / Year: 2016
Title: The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a - an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.
Authors: Lim, S.M. / Yeung, K. / Tresaugues, L. / Ling, T.H. / Nordlund, P.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: Acid sphingomyelinase-like phosphodiesterase 3a
B: Acid sphingomyelinase-like phosphodiesterase 3a
C: Acid sphingomyelinase-like phosphodiesterase 3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,70823
Polymers139,8343
Non-polymers2,87420
Water5,423301
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A: Acid sphingomyelinase-like phosphodiesterase 3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5087
Polymers46,6111
Non-polymers8966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acid sphingomyelinase-like phosphodiesterase 3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6008
Polymers46,6111
Non-polymers9897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acid sphingomyelinase-like phosphodiesterase 3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6008
Polymers46,6111
Non-polymers9897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.790, 147.790, 139.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-807-

HOH

21A-855-

HOH

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Components

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Protein / Sugars , 2 types, 12 molecules ABC

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


Mass: 46611.406 Da / Num. of mol.: 3 / Fragment: UNP residues 34-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMPDL3A, ASML3A / Plasmid: pFB-Sec-NH / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92484, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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, 312 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 2.08 M disodium malonate pH 7.2, 0.23 M sodium thiocyanate and 0.01 M TCEP
PH range: 7.2

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 2.6→48.46 Å / Num. all: 61111 / Num. obs: 54349 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.8
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDS10.9.5data reduction
autoSHARP2.6phasing
Aimless0.3.11data scaling
Coot0.8model building
ARP7model building
RefinementMethod to determine structure: SAD / Resolution: 2.6→48.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 9.106 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.647 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25474 2760 5.1 %RANDOM
Rwork0.23712 ---
obs0.23803 51505 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.786 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å20 Å2
2---0.15 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9864 0 165 301 10330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0210405
X-RAY DIFFRACTIONr_bond_other_d0.0020.029571
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.9614212
X-RAY DIFFRACTIONr_angle_other_deg2.13.00722138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46551257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.2225.525476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.035151664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1411518
X-RAY DIFFRACTIONr_chiral_restr0.1170.21598
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111747
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022367
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8652.0434968
X-RAY DIFFRACTIONr_mcbond_other1.8652.0434967
X-RAY DIFFRACTIONr_mcangle_it3.0253.066221
X-RAY DIFFRACTIONr_mcangle_other3.0243.066222
X-RAY DIFFRACTIONr_scbond_it2.4522.2865437
X-RAY DIFFRACTIONr_scbond_other2.4522.2875438
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9323.3257984
X-RAY DIFFRACTIONr_long_range_B_refined5.73616.76512410
X-RAY DIFFRACTIONr_long_range_B_other5.73616.76812411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 190 -
Rwork0.292 3757 -
obs--99.82 %

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