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- PDB-9c20: The Sialidase NanJ in complex with Neu5,9Ac -

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Basic information

Entry
Database: PDB / ID: 9c20
TitleThe Sialidase NanJ in complex with Neu5,9Ac
Componentsexo-alpha-sialidase
KeywordsHYDROLASE / Sialidase / Glycoside Hydrolase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate binding / intracellular membrane-bounded organelle / metal ion binding / membrane / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / CBM2/CBM3, carbohydrate-binding domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain ...Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / CBM2/CBM3, carbohydrate-binding domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Sialidase superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-5N6 / exo-alpha-sialidase
Similarity search - Component
Biological speciesClostridium perfringens ATCC 13124 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsMedley, B.J. / Low, K.E. / Garber, J.M. / Gray, T.E. / Leeann, L.L. / Fordwour, O.B. / Inglis, G.D. / Boons, G.J. / Zandberg, W.F. / Abbott, W. / Boraston, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Glycomics Network (GLYCONET) Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: A "terminal" case of glycan catabolism: Structural and enzymatic characterization of the sialidases of Clostridium perfringens.
Authors: Medley, B.J. / Low, K.E. / Irungu, J.D.W. / Kipchumba, L. / Daneshgar, P. / Liu, L. / Garber, J.M. / Klassen, L. / Inglis, G.D. / Boons, G.J. / Zandberg, W.F. / Abbott, D.W. / Boraston, A.B.
History
DepositionMay 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _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: exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6873
Polymers50,2731
Non-polymers4132
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.037, 171.037, 93.296
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-1156-

HOH

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Components

#1: Protein exo-alpha-sialidase


Mass: 50273.184 Da / Num. of mol.: 1 / Mutation: R501K,Q534E,K580N,D617G,I620V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria)
Gene: nanJ, CPF_0532 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2YT71, exo-alpha-sialidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar ChemComp-5N6 / 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / (2~{R},4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-3-acetyloxy-1,2-bis(oxidanyl)propyl]-2,4-bis(oxidanyl)oxane-2-ca rboxylic acid / 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid / 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid / 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 351.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21NO10 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Neup5Ac9AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.92 Å3/Da / Density % sol: 68.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 2.0M (NH4)2S04

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→24.81 Å / Num. obs: 47174 / % possible obs: 99.14 % / Redundancy: 5.3 % / CC1/2: 0.935 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.1 Å / Num. unique obs: 1342 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.699→24.808 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.151 / SU B: 10.108 / SU ML: 0.198 / Average fsc free: 0.9513 / Average fsc work: 0.9746 / Cross valid method: FREE R-VALUE / ESU R: 0.382 / ESU R Free: 0.291 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2537 1156 5.153 %
Rwork0.1838 21277 -
all0.187 --
obs-22433 99.143 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.876 Å2
Baniso -1Baniso -2Baniso -3
1-0.349 Å20.175 Å20 Å2
2--0.349 Å20 Å2
3----1.133 Å2
Refinement stepCycle: LAST / Resolution: 2.699→24.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 28 208 3692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123563
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6674836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7845450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.358514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42410531
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.91710169
X-RAY DIFFRACTIONr_chiral_restr0.110.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022784
X-RAY DIFFRACTIONr_nbd_refined0.2250.21692
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.228
X-RAY DIFFRACTIONr_mcbond_it3.2723.5591801
X-RAY DIFFRACTIONr_mcangle_it5.096.3812248
X-RAY DIFFRACTIONr_scbond_it3.9163.5751762
X-RAY DIFFRACTIONr_scangle_it5.9996.5012588
X-RAY DIFFRACTIONr_lrange_it7.64335.425534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.699-2.7680.264740.26915190.26916160.9530.96298.57670.213
2.768-2.8430.414950.26914800.27815800.9210.96499.68350.208
2.843-2.9250.34800.26814480.27215360.930.95899.47920.21
2.925-3.0130.369760.25814080.26414930.9130.95999.39720.206
3.013-3.1110.336670.23813930.24214650.9370.96499.65870.187
3.111-3.2180.321790.22513180.2313980.9320.96899.92850.185
3.218-3.3370.281690.21512930.21913650.9490.9799.78020.182
3.337-3.4710.34590.20312470.20813090.9210.97799.77080.174
3.471-3.6220.262720.19611950.212680.9590.97999.92110.171
3.622-3.7950.23590.16511440.16912060.9670.98699.75120.147
3.795-3.9950.202610.15310800.15511560.9750.98798.70240.13
3.995-4.230.213540.13910400.14211130.9750.98898.29290.118
4.23-4.5130.189500.1159870.11810440.9820.99299.32950.102
4.513-4.8610.151590.1019030.1049790.9870.99498.26350.09
4.861-5.3050.201420.1218560.1249020.9810.99199.55650.106
5.305-5.8980.202430.1617940.1648390.9790.98599.76160.142
5.898-6.7470.208420.1916990.1927450.9720.97999.46310.17
6.747-8.1140.274270.2116220.2136520.9560.97599.53990.192
8.114-10.9070.232250.1775080.1795370.9580.97999.25510.168
10.907-24.8080.234230.1923430.1943740.9690.97497.8610.195

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