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- PDB-8u5o: The structure of the catalytic domain of NanI sialdase in complex... -

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Basic information

Entry
Database: PDB / ID: 8u5o
TitleThe structure of the catalytic domain of NanI sialdase in complex with Neu5Gc
ComponentsExo-alpha-sialidase
KeywordsHYDROLASE / Sialidase
Function / homologyN-glycolyl-alpha-neuraminic acid / NITRATE ION / :
Function and homology information
Biological speciesClostridium perfringens ATCC 13124 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMedley, B.J. / Low, K.E. / Garber, J.M. / Gray, T.E. / Liu, L. / Klassen, L. / Fordwour, O.B. / Inglis, G.D. / Boons, G.J. / Zandberg, W.F. ...Medley, B.J. / Low, K.E. / Garber, J.M. / Gray, T.E. / Liu, L. / Klassen, L. / Fordwour, O.B. / Inglis, G.D. / Boons, G.J. / Zandberg, W.F. / Abbott, W.D. / 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 12, 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: Exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,03411
Polymers50,1951
Non-polymers83910
Water10,917606
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.270, 72.305, 97.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exo-alpha-sialidase


Mass: 50194.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria)
Gene: nanI, CYK96_07055, NCTC10578_00772 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z3TZA2, exo-alpha-sialidase
#2: Sugar ChemComp-NGC / N-glycolyl-alpha-neuraminic acid / N-glycolylneuraminic acid / sialic acid / 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid


Type: D-saccharide, alpha linking / Mass: 325.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO10 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5GcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-glycolyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5GcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5GcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M KNO3, pH 7.0, 15mM Neu5Gc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.542 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: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 77611 / % possible obs: 98.3 % / Redundancy: 4 % / CC1/2: 0.998 / Net I/σ(I): 23.5
Reflection shellResolution: 1.5→20 Å / Num. unique obs: 3256 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.88 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1782 3948 5.11 %
Rwork0.154 --
obs0.1553 77240 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 52 606 4169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013677
X-RAY DIFFRACTIONf_angle_d1.1584986
X-RAY DIFFRACTIONf_dihedral_angle_d7.935510
X-RAY DIFFRACTIONf_chiral_restr0.106538
X-RAY DIFFRACTIONf_plane_restr0.01659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.20811350.19142091X-RAY DIFFRACTION80
1.52-1.540.20441280.16982497X-RAY DIFFRACTION94
1.54-1.560.20091300.16642532X-RAY DIFFRACTION97
1.56-1.580.19431340.16052536X-RAY DIFFRACTION96
1.58-1.60.18721270.15612576X-RAY DIFFRACTION98
1.6-1.630.1891560.15922566X-RAY DIFFRACTION98
1.63-1.650.21181330.1572615X-RAY DIFFRACTION98
1.65-1.680.1621120.15722650X-RAY DIFFRACTION99
1.68-1.710.23261520.15872608X-RAY DIFFRACTION99
1.71-1.740.2411230.17172606X-RAY DIFFRACTION98
1.74-1.770.20971380.16352607X-RAY DIFFRACTION99
1.77-1.810.20061440.15662637X-RAY DIFFRACTION99
1.81-1.850.19061320.15952583X-RAY DIFFRACTION99
1.85-1.890.18231360.16822630X-RAY DIFFRACTION99
1.89-1.940.2091420.15662660X-RAY DIFFRACTION100
1.94-1.990.20111440.16082626X-RAY DIFFRACTION100
1.99-2.050.18451480.15622647X-RAY DIFFRACTION100
2.05-2.110.19241330.15382681X-RAY DIFFRACTION100
2.11-2.190.15991200.15062682X-RAY DIFFRACTION100
2.19-2.280.19041220.14342680X-RAY DIFFRACTION100
2.28-2.380.19071640.14972653X-RAY DIFFRACTION100
2.38-2.510.19671780.15622634X-RAY DIFFRACTION100
2.51-2.660.17511290.16572680X-RAY DIFFRACTION100
2.66-2.870.19521600.16542652X-RAY DIFFRACTION99
2.87-3.150.18341430.16082669X-RAY DIFFRACTION99
3.15-3.610.15941730.14742707X-RAY DIFFRACTION100
3.61-4.540.15741620.1322715X-RAY DIFFRACTION100
4.54-19.880.12471500.14832872X-RAY DIFFRACTION100

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