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- PDB-1snt: Structure of the human cytosolic sialidase Neu2 -

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Basic information

Entry
Database: PDB / ID: 1snt
TitleStructure of the human cytosolic sialidase Neu2
ComponentsSialidase 2
KeywordsHYDROLASE / sialidase / neuraminidase / ganglioside
Function / homology
Function and homology information


Sialic acid metabolism / glycosphingolipid catabolic process / glycoprotein catabolic process / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / catalytic complex / lysosome ...Sialic acid metabolism / glycosphingolipid catabolic process / glycoprotein catabolic process / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChavas, L.M.G. / Fusi, P. / Tringali, C. / Venerando, B. / Tettamanti, G. / Kato, R. / Monti, E. / Wakatsuki, S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of the Human Cytosolic Sialidase Neu2: EVIDENCE FOR THE DYNAMIC NATURE OF SUBSTRATE RECOGNITION
Authors: Chavas, L.M.G. / Tringali, C. / Fusi, P. / Venerando, B. / Tettamanti, G. / Kato, R. / Monti, E. / Wakatsuki, S.
History
DepositionMar 12, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialidase 2


Theoretical massNumber of molelcules
Total (without water)42,4201
Polymers42,4201
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.940, 145.940, 64.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Sialidase 2 / Neu2 / Cytosolic sialidase / N-acetyl-alpha- neuraminidase 2


Mass: 42419.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y3R4, exo-alpha-sialidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: sodium potassium phosphate, sodium chloride, pH 6.2, 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: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. all: 51301 / Num. obs: 51297 / % possible obs: 99.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 5.5
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EUS

1eus


Resolution: 1.75→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: About CD1/CD2 (LEU A 90) and CG1/CG2 (VAL A 325), there are 3 possible positions for these atoms. There are two different conformations for each atom. For convenience, the author assigned as ...Details: About CD1/CD2 (LEU A 90) and CG1/CG2 (VAL A 325), there are 3 possible positions for these atoms. There are two different conformations for each atom. For convenience, the author assigned as a double conformation only one of the atoms.(CD2 of LEU 90 and CG1 of VAL 325) Thus the occupancies of the alternate conformations are greater than 1.00 and there are chirality errors at these atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2551 -RANDOM
Rwork0.201 ---
all0.203 51301 --
obs0.203 51297 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 0 377 3145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.467

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