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- PDB-8f9r: Rabbit sialic acid esterase (SIAE) -

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Basic information

Entry
Database: PDB / ID: 8f9r
TitleRabbit 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 / Sialic acid acetylesterase
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 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: Rabbit 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

Downloads & links

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Assembly

Deposited unit
A: Sialic acid acetylesterase
B: Sialic acid acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,63214
Polymers114,2482
Non-polymers8,38412
Water1629
1
A: Sialic acid acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2357
Polymers57,1241
Non-polymers4,1116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialic acid acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3977
Polymers57,1241
Non-polymers4,2736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.070, 152.690, 81.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 22 through 511 or resid 515 through 533))
d_2ens_1(chain "B" and (resid 22 through 511 or resid 515 through 533))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSILEA1 - 490
d_12ens_1NAGMANC
d_13ens_1NAGFUCD
d_14ens_1NAGMANE
d_15ens_1NAGMANF
d_16ens_1NAGNAGG
d_17ens_1NAGNAGM
d_21ens_1LYSILEB1 - 490
d_22ens_1NAGMANH
d_23ens_1NAGFUCI
d_24ens_1NAGMANJ
d_25ens_1NAGMANK
d_26ens_1NAGBMAL
d_27ens_1NAGNAGN

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Components

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Protein / Non-polymers , 2 types, 11 molecules AB

#1: Protein Sialic acid acetylesterase


Mass: 57123.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: SIAE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5F9D0N0
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 12 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: 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-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
#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}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.: 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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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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium phosphate, 0.1 M Tris, pH 8.5, 50% v/v MPD

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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: 2.95→50 Å / Num. obs: 59316 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 61.56 Å2 / Rrim(I) all: 0.184 / Net I/σ(I): 14.3
Reflection shellResolution: 2.95→3.06 Å / Num. unique obs: 5810 / CC1/2: 0.314

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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: 2.97→50 Å / SU ML: 0.3029 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 2941 8.57 %
Rwork0.2056 31379 -
obs0.2088 34320 60.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.22 Å2
Refinement stepCycle: LAST / Resolution: 2.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7838 0 559 9 8406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00438635
X-RAY DIFFRACTIONf_angle_d0.701111769
X-RAY DIFFRACTIONf_chiral_restr0.05031399
X-RAY DIFFRACTIONf_plane_restr0.00681442
X-RAY DIFFRACTIONf_dihedral_angle_d15.01343296
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.342957553383 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.020.3625110.3713126X-RAY DIFFRACTION5.06
3.02-3.070.4714220.3807230X-RAY DIFFRACTION9.43
3.07-3.130.4361310.3571320X-RAY DIFFRACTION13.2
3.13-3.190.3674410.3259438X-RAY DIFFRACTION17.55
3.19-3.260.3452520.3157539X-RAY DIFFRACTION21.97
3.26-3.330.3133660.3149700X-RAY DIFFRACTION28.71
3.33-3.40.2863800.3089867X-RAY DIFFRACTION34.82
3.4-3.490.3379950.29791023X-RAY DIFFRACTION41.95
3.49-3.580.28121160.28091228X-RAY DIFFRACTION49.47
3.58-3.690.2951300.2531407X-RAY DIFFRACTION56.78
3.69-3.810.27571390.24271533X-RAY DIFFRACTION62.41
3.81-3.940.25721570.20561721X-RAY DIFFRACTION69.81
3.94-4.10.22411900.1961934X-RAY DIFFRACTION78.26
4.1-4.290.23831960.18642128X-RAY DIFFRACTION86.49
4.29-4.510.21292240.16692432X-RAY DIFFRACTION97.86
4.51-4.80.23482380.17372465X-RAY DIFFRACTION100
4.8-5.170.23082340.17812450X-RAY DIFFRACTION99.81
5.17-5.690.24232230.19212454X-RAY DIFFRACTION99.85
5.69-6.510.22762260.21542476X-RAY DIFFRACTION99.85
6.51-8.190.21222310.19532486X-RAY DIFFRACTION99.93
8.19-500.2292390.2012422X-RAY DIFFRACTION98.74

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