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- PDB-2sil: THE STRUCTURES OF SALMONELLA TYPHIMURIUM LT2 NEURAMINIDASE AND IT... -

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Basic information

Entry
Database: PDB / ID: 2sil
TitleTHE STRUCTURES OF SALMONELLA TYPHIMURIUM LT2 NEURAMINIDASE AND ITS COMPLEX WITH A TRANSITION STATE ANALOGUE AT 1.6 ANGSTROMS RESOLUTION
ComponentsSIALIDASE
KeywordsHYDROLASE
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsTaylor, G.L. / Crennell, S.J. / Garman, E.F. / Vimr, E.R. / Laver, W.G.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The structures of Salmonella typhimurium LT2 neuraminidase and its complexes with three inhibitors at high resolution.
Authors: Crennell, S.J. / Garman, E.F. / Philippon, C. / Vasella, A. / Laver, W.G. / Vimr, E.R. / Taylor, G.L.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of a Bacterial Sialidase (from Salmonella Typhimurium Lt2) Shows the Same Fold as an Influenza Virus Neuraminidase
Authors: Crennell, S.J. / Garman, E.F. / Laver, W.G. / Vimr, E.R. / Taylor, G.L.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Purification, Crystallisation and Preliminary Crystallographic Study of Neuraminidase from Vibrio Cholerae and Salmonella Typhimurium
Authors: Taylor, G.L. / Vimr, E.R. / Garman, E.F. / Laver, W.G.
History
DepositionJul 13, 1994Processing site: BNL
SupersessionAug 31, 1994ID: 1SIL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIALIDASE


Theoretical massNumber of molelcules
Total (without water)41,9921
Polymers41,9921
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.500, 82.500, 91.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 136

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Components

#1: Protein SIALIDASE


Mass: 41991.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: PSX62 / Plasmid: PSX62 / References: UniProt: P29768, exo-alpha-sialidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlneuraminidase1drop
21.9 Mpotassium phosphate1drop
32.1 Mpotassium phosphate1reservoir

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Data collection

ReflectionNum. obs: 59728 / % possible obs: 55.9 % / Observed criterion σ(I): 3
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 35140 / % possible obs: 69.6 % / Redundancy: 1.7 % / Num. measured all: 59728 / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.6→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.166 -
obs0.166 35140
Displacement parametersBiso mean: 16.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 0 195 3149
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.17
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
Refinement
*PLUS
Rfactor obs: 0.163 / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_planar_d / Dev ideal: 0.017

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