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- PDB-8f9p: Dog sialic acid esterase (SIAE) inactive mutant S128A -

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Basic information

Entry
Database: PDB / ID: 8f9p
TitleDog sialic acid esterase (SIAE) inactive mutant S128A
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 / sialate O-acetylesterase / SGNH hydrolase superfamily / lysosome / ACETATE ION / Sialate O-acetylesterase
Function and homology information
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsIde, D. / Gorelik, A. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)250057 Canada
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Structural Analysis of Mammalian Sialic Acid Esterase.
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
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Oct 23, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialic acid acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7027
Polymers56,1581
Non-polymers1,5446
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint31 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.045, 111.085, 124.198
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-1093-

HOH

21A-1248-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sialic acid acetylesterase


Mass: 56157.590 Da / Num. of mol.: 1 / Mutation: S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8C0LZX8

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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.: 2
Source method: isolated from a genetically manipulated source
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.: 2 / 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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Non-polymers , 3 types, 596 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium HEPES, pH 7.5, 30% v/v PEG400

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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: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 216052 / % possible obs: 98 % / Redundancy: 10.5 % / Biso Wilson estimate: 14.25 Å2 / Rrim(I) all: 0.098 / Net I/σ(I): 21.8
Reflection shellResolution: 1.55→1.61 Å / Num. unique obs: 17518 / CC1/2: 0.27

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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: 1.55→48.54 Å / SU ML: 0.1328 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.7467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1462 2900 2.13 %
Rwork0.1174 133404 -
obs0.118 136304 63.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.18 Å2
Refinement stepCycle: LAST / Resolution: 1.55→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 101 594 4558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074108
X-RAY DIFFRACTIONf_angle_d0.95325596
X-RAY DIFFRACTIONf_chiral_restr0.0542617
X-RAY DIFFRACTIONf_plane_restr0.0071711
X-RAY DIFFRACTIONf_dihedral_angle_d14.06361483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.616970.3905339X-RAY DIFFRACTION3.39
1.57-1.60.3773220.33271043X-RAY DIFFRACTION10.52
1.6-1.630.3212480.29052043X-RAY DIFFRACTION20.55
1.63-1.660.2399710.25473321X-RAY DIFFRACTION33.03
1.66-1.690.2925920.2194112X-RAY DIFFRACTION41.46
1.69-1.730.257940.1984510X-RAY DIFFRACTION45.32
1.73-1.770.2271060.17024804X-RAY DIFFRACTION48.33
1.77-1.810.21841070.15715020X-RAY DIFFRACTION50.43
1.81-1.860.19441120.14115079X-RAY DIFFRACTION51.3
1.86-1.920.17831150.12835293X-RAY DIFFRACTION52.65
1.92-1.980.12961220.11235632X-RAY DIFFRACTION56.8
1.98-2.050.11821380.09536392X-RAY DIFFRACTION64.39
2.05-2.130.13581640.08827551X-RAY DIFFRACTION75.7
2.13-2.230.13471820.08698861X-RAY DIFFRACTION88.76
2.23-2.350.13012180.08759760X-RAY DIFFRACTION98.36
2.35-2.490.13222030.09149945X-RAY DIFFRACTION99.59
2.49-2.690.13362130.09299929X-RAY DIFFRACTION99.76
2.69-2.960.12922160.10319937X-RAY DIFFRACTION99.84
2.96-3.380.13782170.11969939X-RAY DIFFRACTION99.9
3.38-4.260.11382210.11129952X-RAY DIFFRACTION100
4.26-48.540.17262320.15099942X-RAY DIFFRACTION99.87

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