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- PDB-4nc5: Human sialidase 2 in complex with 2,3-difluorosialic acid (covale... -

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Basic information

Entry
Database: PDB / ID: 4nc5
TitleHuman sialidase 2 in complex with 2,3-difluorosialic acid (covalent intermediate)
ComponentsSialidase-2
KeywordsHYDROLASE / Human neuraminidase / sialidase
Function / homology
Function and homology information


Sialic acid metabolism / glycoprotein catabolic process / glycosphingolipid catabolic process / exo-alpha-sialidase activity / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity ...Sialic acid metabolism / glycoprotein catabolic process / glycosphingolipid catabolic process / exo-alpha-sialidase activity / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / catalytic complex / lysosome / membrane / cytosol / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-FSI / PHOSPHATE ION / Sialidase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.513 Å
AuthorsBuchini, S. / Gallat, F.-X. / Greig, I.R. / Kim, J.-H. / Wakatsuki, S. / Chavas, L.M.G. / Withers, S.G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Tuning mechanism-based inactivators of neuraminidases: mechanistic and structural insights.
Authors: Buchini, S. / Gallat, F.X. / Greig, I.R. / Kim, J.H. / Wakatsuki, S. / Chavas, L.M. / Withers, S.G.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialidase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8934
Polymers42,3761
Non-polymers5173
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.408, 87.916, 92.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sialidase-2 / / NEU2 / Cytosolic sialidase / N-acetyl-alpha-neuraminidase 2


Mass: 42375.586 Da / Num. of mol.: 1 / Mutation: D46A,H168N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEU2 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y3R4, exo-alpha-sialidase
#2: Sugar ChemComp-FSI / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 3-FLUOROSIALIC ACID / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-manno-non-2-ulosonic acid


Type: D-saccharide, beta linking / Mass: 327.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H18FNO9
IdentifierTypeProgram
b-D-Neup5Ac3fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: SODIUM/POTASSIUM PHOSPHATE BUFFER, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 9, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.513→46.2 Å / Num. all: 11940 / Num. obs: 11706 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.513→2.578 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.32refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VCU

1vcu


Resolution: 2.513→46.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.891 / SU B: 11.023 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26311 597 4.9 %RANDOM
Rwork0.17408 ---
obs0.1784 11706 98.82 %-
all-11940 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.561 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.81 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.513→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 31 103 2919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192913
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9593979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0695355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02323.165139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28115433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8741524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212279
X-RAY DIFFRACTIONr_mcbond_it2.5653.5681422
X-RAY DIFFRACTIONr_mcangle_it4.125.3241773
X-RAY DIFFRACTIONr_scbond_it3.2033.8781491
X-RAY DIFFRACTIONr_long_range_B_refined8.20130.4824431
LS refinement shellResolution: 2.513→2.578 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 40 -
Rwork0.23 791 -
obs--91.42 %

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