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- PDB-1so7: Maltose-induced structure of the human cytolsolic sialidase Neu2 -

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Basic information

Entry
Database: PDB / ID: 1so7
TitleMaltose-induced structure of the human cytolsolic sialidase Neu2
ComponentsSialidase 2
KeywordsHYDROLASE / sialidase / neuraminidase / ganglioside / sugar-induced form
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 / cytoplasm / cytosol
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: 1.49 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4552
Polymers42,4201
Non-polymers351
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.690, 145.690, 64.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-461-

HOH

31A-613-

HOH

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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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 58.33 %
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: 1.49→50 Å / Num. all: 83517 / Num. obs: 79480 / % possible obs: 97 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.3
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.9 / % possible all: 85.8

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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 1SNT

1snt


Resolution: 1.49→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: About CD1/CD2 (LEU A 90), OE1/OE2 (GLU A 218) and CG1/CG2 (VAL A 325), there are 3 possible positions for these atoms. There are two different conformations for each atom. For convenience, ...Details: About CD1/CD2 (LEU A 90), OE1/OE2 (GLU A 218) 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, OE1 of GLU 218 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. The chirality errors appear at CB (ILE A 105) and CG (BLEU A 365). About LEU 365, the author could see two conformations, but only the atom CG was obvious. The other atoms (respectively CD1 and CD2), if in an other conformation, would have been too close than the first conformation. The author only applied two conformations for the CG atom. About ILE 105, the author could see density for an other conformation only for a CG atom, but nothing for the CD1. The author assigned only 2 conformations for the CG2 atom. These are the reasons for the chirality errors.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4011 -RANDOM
Rwork0.202 ---
all0.203 83517 --
obs0.203 79480 97 %-
Refinement stepCycle: LAST / Resolution: 1.49→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 1 296 3144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.633

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