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- PDB-8w6r: murine SMPDL3A bound to sulfate -

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Basic information

Entry
Database: PDB / ID: 8w6r
Titlemurine SMPDL3A bound to sulfate
ComponentsAcid sphingomyelinase-like phosphodiesterase 3a
KeywordsHYDROLASE / innate immunity / lipid metabolism
Function / homology
Function and homology information


nucleoside triphosphate catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / negative regulation of cGAS/STING signaling pathway / nucleoside-triphosphate phosphatase / ATP hydrolysis activity / extracellular space / extracellular region / zinc ion binding
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
Cyclic GMP-AMP phosphodiesterase SMPDL3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, C. / Liu, P. / Fan, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070875 China
National Natural Science Foundation of China (NSFC)82241074 China
CitationJournal: Immunity / Year: 2023
Title: SMPDL3A is a cGAMP-degrading enzyme induced by LXR-mediated lipid metabolism to restrict cGAS-STING DNA sensing.
Authors: Hou, Y. / Wang, Z. / Liu, P. / Wei, X. / Zhang, Z. / Fan, S. / Zhang, L. / Han, F. / Song, Y. / Chu, L. / Zhang, C.
History
DepositionAug 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8568
Polymers47,5411
Non-polymers1,3157
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-81 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.374, 86.374, 79.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 47540.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smpdl3a, Asml3a / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P70158, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Sugars , 2 types, 4 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: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: 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: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 369 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.1 M sodium citrate [pH 5.5], 0.2M ammonium sulfate and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20.54 Å / Num. obs: 42004 / % possible obs: 97.7 % / Redundancy: 9.1 % / Biso Wilson estimate: 21.61 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.157 / Net I/σ(I): 27.6
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2041 / CC1/2: 0.733 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
PDB_EXTRACTdata extraction
PHENIXmodel building
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→20.54 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 2054 4.95 %
Rwork0.2212 --
obs0.2229 41529 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→20.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 77 366 3722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093447
X-RAY DIFFRACTIONf_angle_d1.2444708
X-RAY DIFFRACTIONf_dihedral_angle_d10.455474
X-RAY DIFFRACTIONf_chiral_restr0.062533
X-RAY DIFFRACTIONf_plane_restr0.008594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.32731440.26612633X-RAY DIFFRACTION97
1.99-2.040.33611310.25232682X-RAY DIFFRACTION100
2.04-2.10.28721030.22582757X-RAY DIFFRACTION100
2.1-2.160.31471040.21072734X-RAY DIFFRACTION100
2.16-2.230.25931280.22872718X-RAY DIFFRACTION100
2.23-2.310.32071310.23582713X-RAY DIFFRACTION100
2.31-2.40.26231330.22932728X-RAY DIFFRACTION99
2.4-2.510.34421350.25142635X-RAY DIFFRACTION98
2.51-2.640.27161550.22962690X-RAY DIFFRACTION99
2.64-2.810.24641610.20172696X-RAY DIFFRACTION100
2.81-3.020.23071310.20352732X-RAY DIFFRACTION100
3.02-3.330.25751460.20252708X-RAY DIFFRACTION99
3.33-3.80.28971150.25312012X-RAY DIFFRACTION74
3.81-4.780.19521650.2152296X-RAY DIFFRACTION86
4.79-20.540.19861720.1942741X-RAY DIFFRACTION99

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