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- PDB-1eut: SIALIDASE, LARGE 68KD FORM, COMPLEXED WITH GALACTOSE -

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Basic information

Entry
Database: PDB / ID: 1eut
TitleSIALIDASE, LARGE 68KD FORM, COMPLEXED WITH GALACTOSE
ComponentsSIALIDASENeuraminidase
KeywordsHYDROLASE / GLYCOSIDASE
Function / homology
Function and homology information


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 / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm
Similarity search - Function
Alpha-galactosidase, NEW3 domain / NPCBM-associated, NEW3 domain of alpha-galactosidase / BNR repeat-like domain / Sialidase family / Sialidase / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Neuraminidase - #10 ...Alpha-galactosidase, NEW3 domain / NPCBM-associated, NEW3 domain of alpha-galactosidase / BNR repeat-like domain / Sialidase family / Sialidase / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Neuraminidase - #10 / Sialidase superfamily / Galactose-binding domain-like / 6 Propeller / Neuraminidase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Jelly Rolls / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMicromonospora viridifaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsGaskell, A. / Crennell, S.J. / Taylor, G.L.
Citation
Journal: Structure / Year: 1995
Title: The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll.
Authors: Gaskell, A. / Crennell, S. / Taylor, G.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary Crystallographic Study of Neuraminidase from Micromonospora Viridifaciens
Authors: Taylor, G. / Dineley, L. / Glowka, M. / Laver, G.
History
DepositionJun 21, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6722
Polymers64,6491
Non-polymers231
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.280, 117.300, 60.240
Angle α, β, γ (deg.)90.00, 96.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SIALIDASE / Neuraminidase / NEURAMINIDASE


Mass: 64649.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: LARGE 68KD FORM / Source: (natural) Micromonospora viridifaciens (bacteria) / References: UniProt: Q02834, exo-alpha-sialidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 52 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Taylor, G., (1992) J.Mol.Biol., 225, 1135. / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
Conc.: 8 % / Common name: PEG3350

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.993
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionNum. obs: 20112 / % possible obs: 79.2 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.039
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 49584
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å / % possible obs: 76.8 % / Rmerge(I) obs: 0.092

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.5→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.214 -
obs0.214 18632
Displacement parametersBiso mean: 20.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 1 0 4537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.57
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2

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