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- PDB-8um0: The structure of NanH in complex with Neu5,7,9Ac(2,6)-LAcNAc -

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Basic information

Entry
Database: PDB / ID: 8um0
TitleThe structure of NanH in complex with Neu5,7,9Ac(2,6)-LAcNAc
ComponentsSialidase
KeywordsHYDROLASE / Sialidase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / : / : / : / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesClostridium perfringens ATCC 13124 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsMedley, B.J. / Boraston, A.B.
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
DepositionOct 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.title / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,46313
Polymers43,0661
Non-polymers1,39712
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.184, 64.691, 65.578
Angle α, β, γ (deg.)90.00, 102.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sialidase


Mass: 43065.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria)
Gene: nanH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1V1R3
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-X1F / 5-acetamido-7,9-di-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid


Mass: 393.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO11
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES:NaOH pH 7.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.46→24 Å / Num. obs: 25987 / % possible obs: 99.3 % / Redundancy: 3.9 % / CC1/2: 0.993 / Net I/σ(I): 16.1
Reflection shellResolution: 2.46→2.65 Å / Num. unique obs: 1267 / CC1/2: 0.815

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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: 2.46→23.8 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 674 5.12 %
Rwork0.1898 --
obs0.1924 13154 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 92 129 3036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.4813999
X-RAY DIFFRACTIONf_dihedral_angle_d4.666455
X-RAY DIFFRACTIONf_chiral_restr0.045438
X-RAY DIFFRACTIONf_plane_restr0.003507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.650.30521150.23832259X-RAY DIFFRACTION87
2.65-2.920.30931410.23782584X-RAY DIFFRACTION98
2.92-3.340.25081290.21322564X-RAY DIFFRACTION97
3.34-4.20.21481460.17142523X-RAY DIFFRACTION96
4.2-23.80.21061430.16412550X-RAY DIFFRACTION95

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