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- PDB-8url: The Apo NanJ structure from Clostridium perfringens -

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Basic information

Entry
Database: PDB / ID: 8url
TitleThe Apo NanJ structure from Clostridium perfringens
ComponentsExo-alpha-sialidase NanJ
KeywordsHYDROLASE / Sialidase
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 26, 2023Deposition 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

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Assembly

Deposited unit
A: Exo-alpha-sialidase NanJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1283
Polymers50,0481
Non-polymers802
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.226, 48.804, 73.324
Angle α, β, γ (deg.)90.000, 93.948, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Exo-alpha-sialidase NanJ


Mass: 50047.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: nanJ / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5 2.0M (NH4)2SO4

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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 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→23 Å / Num. obs: 23654 / % possible obs: 99.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 32.59 Å2 / CC1/2: 0.992 / Net I/σ(I): 12.5
Reflection shellResolution: 2.2→2.3 Å / Num. unique obs: 1095 / CC1/2: 0.909

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Processing

Software
NameVersionClassification
PHENIX3.7refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→22.89 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2485 1126 4.9 %
Rwork0.2009 21838 -
obs0.2032 22964 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 2 80 3467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693464
X-RAY DIFFRACTIONf_angle_d0.87294692
X-RAY DIFFRACTIONf_chiral_restr0.0572493
X-RAY DIFFRACTIONf_plane_restr0.0081619
X-RAY DIFFRACTIONf_dihedral_angle_d13.57611239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.3012970.21962164X-RAY DIFFRACTION75.09
2.3-2.420.28851260.22792683X-RAY DIFFRACTION94.26
2.42-2.570.29031490.24792842X-RAY DIFFRACTION98.68
2.57-2.770.30381550.24252796X-RAY DIFFRACTION99.23
2.77-3.040.28641640.24462836X-RAY DIFFRACTION99.17
3.04-3.480.24661330.20982842X-RAY DIFFRACTION98.94
3.48-4.380.22051440.17172813X-RAY DIFFRACTION97.66
4.38-22.890.2131580.17052862X-RAY DIFFRACTION97.11

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