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- PDB-1ms3: Monoclinic form of Trypanosoma cruzi trans-sialidase -

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Basic information

Entry
Database: PDB / ID: 1ms3
TitleMonoclinic form of Trypanosoma cruzi trans-sialidase
Componentstrans-sialidase
KeywordsHYDROLASE / transglycosylation / beta-propeller / protein-carbohydrate interactions / sialidase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase ...: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Trans-sialidase / Trans-sialidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBuschiazzo, A. / Amaya, M.F. / Cremona, M.L. / Frasch, A.C. / Alzari, P.M.
CitationJournal: 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
DepositionSep 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: trans-sialidase
B: trans-sialidase


Theoretical massNumber of molelcules
Total (without water)142,7792
Polymers142,7792
Non-polymers00
Water20,7531152
1
A: trans-sialidase


Theoretical massNumber of molelcules
Total (without water)71,3891
Polymers71,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: trans-sialidase


Theoretical massNumber of molelcules
Total (without water)71,3891
Polymers71,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.215, 128.847, 86.618
Angle α, β, γ (deg.)90.00, 90.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein trans-sialidase


Mass: 71389.258 Da / Num. of mol.: 2 / Fragment: enzymatic globular core / Mutation: N58F,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): DH5a-FT
References: UniProt: Q26964, UniProt: Q26966*PLUS, exo-alpha-sialidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1152 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, TrisHCl, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mMDANA11
22 Mammonium sulfate11
3100 mMHEPES11pH8.
42 %PEG40011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.966 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 166779 / Num. obs: 166779 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.09
Reflection shellResolution: 1.65→1.68 Å / Rsym value: 0.393 / % possible all: 72.8
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 72.8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 1MZ5

1mz5


Resolution: 1.65→14.97 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19198 8341 5 %RANDOM
Rwork0.16295 ---
all0.16441 158211 --
obs0.16441 158211 94.75 %-
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: 20.385 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9808 0 0 1152 10960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02110056
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.93413724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21431295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53151744
X-RAY DIFFRACTIONr_chiral_restr0.1090.21504
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027672
X-RAY DIFFRACTIONr_nbd_refined0.2190.35447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.51830
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.376
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.531
X-RAY DIFFRACTIONr_mcbond_it0.8221.56263
X-RAY DIFFRACTIONr_mcangle_it1.498210163
X-RAY DIFFRACTIONr_scbond_it2.42433793
X-RAY DIFFRACTIONr_scangle_it3.9454.53561
LS refinement shellResolution: 1.65→1.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 338
Rwork0.223 6289
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.91

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