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- PDB-8uvv: The NanJ sialidase catalytic domain in complex with Neu5Ac -

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Basic information

Entry
Database: PDB / ID: 8uvv
TitleThe NanJ sialidase catalytic domain in complex with Neu5Ac
ComponentsExo-alpha-sialidase NanJ
KeywordsHYDROLASE / Sialidase / sialic acid
Function / homologyN-acetyl-alpha-neuraminic acid
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionNov 4, 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 NanJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4284
Polymers50,0481
Non-polymers3803
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.134, 171.134, 92.843
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Components on special symmetry positions
IDModelComponents
11A-902-

CL

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 68.63 %
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-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: 2.5→20 Å / Num. obs: 28058 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 42.09 Å2 / CC1/2: 0.997 / Net I/σ(I): 19
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 28058 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
PHENIX3.7refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.67 Å / SU ML: 0.344 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1325 4.94 %RANDOM
Rwork0.2171 25504 --
obs0.2189 26829 95.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 23 138 3612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233561
X-RAY DIFFRACTIONf_angle_d0.59964837
X-RAY DIFFRACTIONf_chiral_restr0.0457516
X-RAY DIFFRACTIONf_plane_restr0.004639
X-RAY DIFFRACTIONf_dihedral_angle_d16.13841307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.37291420.29972786X-RAY DIFFRACTION95.75
2.6-2.720.35251420.31142773X-RAY DIFFRACTION95.26
2.72-2.860.37891390.30692738X-RAY DIFFRACTION93.41
2.86-3.040.35751580.29562711X-RAY DIFFRACTION93.3
3.04-3.270.3471240.26892822X-RAY DIFFRACTION95.4
3.27-3.60.21761350.22172888X-RAY DIFFRACTION96.98
3.6-4.120.22381680.19062796X-RAY DIFFRACTION94.88
4.12-5.170.18631420.15162882X-RAY DIFFRACTION95.18
5.17-19.670.20711750.18693108X-RAY DIFFRACTION98.5

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