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- PDB-8ub5: The Apo NanH structure from Clostridium perfringens -

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Basic information

Entry
Database: PDB / ID: 8ub5
TitleThe Apo NanH structure from Clostridium perfringens
ComponentsSialidase
KeywordsHYDROLASE / Sialidase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
ACETYL GROUP / exo-alpha-sialidase
Similarity search - Component
Biological speciesClostridium perfringens ATCC 13124 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionSep 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Refinement description / Category: citation / citation_author / software
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 / _software.classification
Revision 1.2Oct 30, 2024Group: Database references / Refinement description / Structure summary
Category: citation / pdbx_entry_details / software
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _pdbx_entry_details.has_protein_modification / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,55329
Polymers43,0671
Non-polymers1,48628
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.436, 64.492, 65.747
Angle α, β, γ (deg.)90.00, 102.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

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Components

#1: Protein Sialidase


Mass: 43066.914 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 45.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M 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 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 35412 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.991 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 1757 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PHASERphasing
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.45 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 1705 4.84 %
Rwork0.1637 --
obs0.1653 35213 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 98 274 3204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112980
X-RAY DIFFRACTIONf_angle_d1.0783996
X-RAY DIFFRACTIONf_dihedral_angle_d7.183415
X-RAY DIFFRACTIONf_chiral_restr0.075433
X-RAY DIFFRACTIONf_plane_restr0.009511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.32931320.25662686X-RAY DIFFRACTION96
1.85-1.910.24111280.19592795X-RAY DIFFRACTION100
1.91-1.980.22691490.16982785X-RAY DIFFRACTION100
1.98-2.060.22221700.16242775X-RAY DIFFRACTION100
2.06-2.150.20641640.16282786X-RAY DIFFRACTION100
2.15-2.270.18891370.14842812X-RAY DIFFRACTION100
2.27-2.410.18271390.15752789X-RAY DIFFRACTION100
2.41-2.590.24051080.16622820X-RAY DIFFRACTION99
2.59-2.850.26341400.17872794X-RAY DIFFRACTION99
2.85-3.270.21191340.17952804X-RAY DIFFRACTION99
3.27-4.110.17551520.1512800X-RAY DIFFRACTION99
4.12-29.450.13611520.14612862X-RAY DIFFRACTION99

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