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- PDB-1ms9: Triclinic form of Trypanosoma cruzi trans-sialidase, in complex w... -

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Basic information

Entry
Database: PDB / ID: 1ms9
TitleTriclinic form of Trypanosoma cruzi trans-sialidase, in complex with lactose
Componentstrans-sialidase
KeywordsHYDROLASE / sialidase / trans-glycosylation / protein-acrbohydrate interactions / beta-propeller
Function / homology
Function and homology information


ganglioside catabolic process / exo-alpha-sialidase activity / oligosaccharide catabolic process / 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 / Jelly Rolls - #200 ...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
beta-lactose / Trans-sialidase / Trans-sialidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 of 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: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,4634
Polymers142,7792
Non-polymers6852
Water21,6181200
1
A: trans-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7322
Polymers71,3891
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: trans-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7322
Polymers71,3891
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.046, 74.204, 87.496
Angle α, β, γ (deg.)86.02, 84.17, 88.31
Int Tables number1
Space group name H-MP1

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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: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1200 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, Tris.HCl, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein11
210 %PEG400011
3100 mMTris-HCl11pH7.5
45 %isopropanol11

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.58→29.4 Å / Num. all: 163610 / Num. obs: 163610 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.038
Reflection shellResolution: 1.58→1.67 Å / Rsym value: 0.125 / % possible all: 82.8
Reflection
*PLUS
Redundancy: 2.2 % / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 82.8 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 1MZ5

1mz5


Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19754 16257 9.9 %RANDOM
Rwork0.16293 ---
all0.1664 147244 --
obs0.1664 147244 94.43 %-
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: 12.887 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9662 0 46 1200 10908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02110174
X-RAY DIFFRACTIONr_bond_other_d0.0010.029046
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9413949
X-RAY DIFFRACTIONr_angle_other_deg0.817321077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9431338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.272151768
X-RAY DIFFRACTIONr_chiral_restr0.1180.21530
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211474
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022118
X-RAY DIFFRACTIONr_nbd_refined0.2160.31746
X-RAY DIFFRACTIONr_nbd_other0.2020.38760
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.51113
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1770.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.357
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.531
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0451.56309
X-RAY DIFFRACTIONr_mcangle_it1.725210303
X-RAY DIFFRACTIONr_scbond_it2.72133865
X-RAY DIFFRACTIONr_scangle_it4.1484.53646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.625 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 874
Rwork0.23 8365
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.85

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