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- PDB-1s0j: Trypanosoma cruzi trans-sialidase in complex with MuNANA (Michael... -

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Basic information

Entry
Database: PDB / ID: 1s0j
TitleTrypanosoma cruzi trans-sialidase in complex with MuNANA (Michaelis complex)
Componentstrans-sialidase
KeywordsHYDROLASE / transglycosidase / Michaelis complex / Trypanosoma cruzi
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / membrane / cytoplasm
Similarity search - Function
: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / 6 Propeller / Neuraminidase / Sialidase superfamily ...: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / 6 Propeller / Neuraminidase / Sialidase superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-MUS / Trans-sialidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAmaya, M.F. / Watts, A.G. / Damager, I. / Wehenkel, A. / Nguyen, T. / Buschiazzo, A. / Paris, G. / Frasch, A.C. / Withers, S.G. / Alzari, P.M.
Citation
Journal: Structure / Year: 2004
Title: Structural Insights into the Catalytic Mechanism of Trypanosoma cruzi trans-Sialidase.
Authors: Amaya, M.F. / Watts, A.G. / Damager, I. / Wehenkel, A. / Nguyen, T. / Buschiazzo, A. / Paris, G. / Frasch, A.C. / Withers, S.G. / Alzari, P.M.
#1: Journal: Mol.Cell / Year: 2002
Title: The crystal structure and mode of action of trans-sialidase, a key enzyme in Trypanosoma cruzi pathogenesis
Authors: Buschiazzo, A. / Amaya, M.F. / Cremona, M.L. / Frasch, A.C. / Alzari, P.M.
History
DepositionDec 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AUTHOR INDICATES THAT THE SEQUENCE IN THE DATABASE IS INCORRECT

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: trans-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8132
Polymers71,3451
Non-polymers4671
Water10,359575
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.373, 129.423, 54.234
Angle α, β, γ (deg.)90.00, 108.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein trans-sialidase


Mass: 71345.250 Da / Num. of mol.: 1 / Mutation: N58F,D59A,S495K,V496G,E520K,D593G,I597D,H599R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10F / References: UniProt: Q26966, exo-alpha-sialidase
#2: Chemical ChemComp-MUS / 4-METHYL-2-OXO-2H-CHROMEN-7-YL 5-(ACETYLAMINO)-3,5-DIDEOXY-L-ERYTHRO-NON-2-ULOPYRANOSIDONIC ACID / METHYLUMBELLIFERYL SIALIC ACID


Mass: 467.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25NO11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Tris-HCl, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 78288 / Num. obs: 78288 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.208 / % possible all: 71.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MS1

1ms1


Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.764 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19365 3897 5 %RANDOM
Rwork0.16152 ---
obs0.16313 74362 91.82 %-
all-74362 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å21.52 Å2
2---0.72 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 33 575 5450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214992
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9446781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4093621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95115865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023777
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.32292
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.5736
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.331
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0051.53083
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76724971
X-RAY DIFFRACTIONr_scbond_it2.71931909
X-RAY DIFFRACTIONr_scangle_it4.3574.51810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.236 203
Rwork0.178 4463

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