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- PDB-8f9o: Dog sialic acid esterase (SIAE) -

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Basic information

Entry
Database: PDB / ID: 8f9o
TitleDog sialic acid esterase (SIAE)
ComponentsSialic acid acetylesterase
KeywordsHYDROLASE / sialic acid / sialate o-acetylesterase
Function / homologySialate O-acetylesterase / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / sialate O-acetylesterase activity / SGNH hydrolase superfamily / Sialate O-acetylesterase domain-containing protein
Function and homology information
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsIde, D. / Gorelik, A. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)250057 Canada
CitationJournal: To Be Published
Title: Dog sialic acid esterase (SIAE)
Authors: Ide, D. / Gorelik, A. / Illes, K. / Nagar, B.
History
DepositionNov 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialic acid acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2116
Polymers56,1741
Non-polymers3,0385
Water15,313850
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.702, 112.480, 122.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1124-

HOH

21A-1253-

HOH

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Components

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Protein / Non-polymers , 2 types, 851 molecules A

#1: Protein Sialic acid acetylesterase


Mass: 56173.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8C0LZX8, sialate O-acetylesterase
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 5 molecules

#2: 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
#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 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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
#6: 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.: 1 / Source method: obtained synthetically / 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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Details

Has ligand of interestN

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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: 3.42 Å3/Da / Density % sol: 64.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.01 M tri-sodium citrate, 16% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 413696 / % possible obs: 98 % / Redundancy: 12.1 % / Biso Wilson estimate: 14.11 Å2 / Rrim(I) all: 0.096 / Net I/σ(I): 27.1
Reflection shellResolution: 1.25→1.29 Å / Num. unique obs: 33962 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→35.85 Å / SU ML: 0.0722 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.2906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1201 3017 1.08 %
Rwork0.1025 275193 -
obs0.1027 278210 67.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.37 Å2
Refinement stepCycle: LAST / Resolution: 1.25→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 202 850 4916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01614244
X-RAY DIFFRACTIONf_angle_d1.4085797
X-RAY DIFFRACTIONf_chiral_restr0.1096675
X-RAY DIFFRACTIONf_plane_restr0.0121720
X-RAY DIFFRACTIONf_dihedral_angle_d13.52111583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.4429160.39741510X-RAY DIFFRACTION8.13
1.27-1.290.3922270.34712522X-RAY DIFFRACTION13.59
1.29-1.310.2826450.26824517X-RAY DIFFRACTION24.43
1.31-1.340.3026640.21856104X-RAY DIFFRACTION32.7
1.34-1.360.1773770.19297406X-RAY DIFFRACTION40.09
1.36-1.390.211890.17458392X-RAY DIFFRACTION45.04
1.39-1.420.18991010.15778807X-RAY DIFFRACTION47.63
1.42-1.450.1747970.14729119X-RAY DIFFRACTION48.98
1.45-1.490.18121040.13499532X-RAY DIFFRACTION51.44
1.49-1.530.12681170.102210338X-RAY DIFFRACTION55.81
1.53-1.570.10391280.084211727X-RAY DIFFRACTION63.06
1.57-1.620.11621520.082813581X-RAY DIFFRACTION73.25
1.62-1.680.11221780.081315958X-RAY DIFFRACTION86.17
1.68-1.750.09841980.081217803X-RAY DIFFRACTION95.85
1.75-1.830.11721980.083318309X-RAY DIFFRACTION98.54
1.83-1.930.10652000.077818464X-RAY DIFFRACTION99.31
1.93-2.050.10591990.07618464X-RAY DIFFRACTION99.56
2.05-2.20.07942040.079718501X-RAY DIFFRACTION99.75
2.2-2.430.1181990.082718534X-RAY DIFFRACTION99.79
2.43-2.780.13482050.100618536X-RAY DIFFRACTION99.82
2.78-3.50.10682070.109218520X-RAY DIFFRACTION99.94
3.5-35.850.13132120.127518549X-RAY DIFFRACTION99.86

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