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- PDB-3sil: SIALIDASE FROM SALMONELLA TYPHIMURIUM -

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Basic information

Entry
Database: PDB / ID: 3sil
TitleSIALIDASE FROM SALMONELLA TYPHIMURIUM
ComponentsSIALIDASE
KeywordsGLYCOSIDASE / HYDROLASE
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
: / PHOSPHATE ION / Sialidase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.05 Å
AuthorsGarman, E.F. / Sheldrick, G.M.
Citation
Journal: To be Published
Title: An Enzyme at Atomic Resolution: The 1.05 A Structure of Salmonella Typhimurium Neuraminidase (Sialidase)
Authors: Garman, E.F. / Wouters, J. / Schneider, T.R. / Vimr, E.R. / Laver, W.G. / Sheldrick, G.M.
#1: 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.
#2: 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.
History
DepositionJul 7, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)42,4789
Polymers41,7921
Non-polymers6878
Water10,106561
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.100, 81.730, 91.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SIALIDASE


Mass: 41791.555 Da / Num. of mol.: 1 / Mutation: RESIDUE MET 1 WAS EXCISED BY ESCHERICHIA COLI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: NANH / Variant: TA263, PROTOTROPH / Plasmid: PSX62 / Gene (production host): NANH / Production host: Escherichia coli (E. coli) / References: UniProt: P29768, exo-alpha-sialidase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growpH: 7.86 / Details: pH 7.86

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.862
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.862 Å / Relative weight: 1
ReflectionResolution: 1.05→11 Å / Num. obs: 148478 / % possible obs: 90.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 8.5
Reflection shellResolution: 1.05→1.15 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.4 / % possible all: 89.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementStarting model: PDB ENTRY 2SIL

2sil


Highest resolution: 1.05 Å / Num. parameters: 33361 / Num. restraintsaints: 41703 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF).
RfactorNum. reflection% reflectionSelection details
Rfree0.1474 4529 3.1 %RANDOM
all0.1162 148474 --
obs0.1163 -90.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. (1973) 91: 201-228
Refine analyzeNum. disordered residues: 47 / Occupancy sum hydrogen: 2797.8 / Occupancy sum non hydrogen: 3526.4
Refinement stepCycle: LAST / Highest resolution: 1.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 42 561 3543
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0.02
X-RAY DIFFRACTIONs_from_restr_planes0.035
X-RAY DIFFRACTIONs_zero_chiral_vol0.127
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.142
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.034
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0.114

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