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- PDB-3pjq: Trypanosoma cruzi trans-sialidase-like inactive isoform (includin... -

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Basic information

Entry
Database: PDB / ID: 3pjq
TitleTrypanosoma cruzi trans-sialidase-like inactive isoform (including the natural mutation Tyr342His) in complex with lactose
ComponentsTrans-sialidase
KeywordsSUGAR BINDING PROTEIN / beta-propeller / lectin / similar to actve trans-sialidases / lactose
Function / homology
Function and homology information


exo-alpha-sialidase activity
Similarity search - Function
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 ...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
alpha-lactose / Trans-sialidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsOppezzo, P. / Baraibar, M. / Obal, G. / Pritsch, O. / Alzari, P.M. / Buschiazzo, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Crystal structure of an enzymatically inactive trans-sialidase-like lectin from Trypanosoma cruzi: the carbohydrate binding mechanism involves residual sialidase activity.
Authors: Oppezzo, P. / Obal, G. / Baraibar, M.A. / Pritsch, O. / Alzari, P.M. / Buschiazzo, A.
History
DepositionNov 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7072
Polymers71,3641
Non-polymers3421
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.391, 130.217, 54.529
Angle α, β, γ (deg.)90.000, 107.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trans-sialidase


Mass: 71364.234 Da / Num. of mol.: 1 / Fragment: unp residues 2-635 / Mutation: N58F,Y342H,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: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE RESIDUES 262, 342, 476, 484 AND 558 ARE NOT CORRECT AT THE CORRESPONDING ...AUTHORS STATE THAT THE RESIDUES 262, 342, 476, 484 AND 558 ARE NOT CORRECT AT THE CORRESPONDING POSITIONS OF UNP ENTRY Q26966. MUTATION TYR342HIS WAS INTRODUCED BY RECOMBINANT DNA TECHNIQUES ONTO AN OTHERWISE TRANS-SIALIDASE SCAFFOLD, RENDERING A CATALYTICALLY INACTIVE FORM THAT MIMICS THE NATURAL INACTIVE TS-LIKE ISOFORMS TRYPANOSOMA CRUZI

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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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: microseeding in 10% PEG 4000, 100mM Tris.HCl, 5% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2004
RadiationMonochromator: diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.965
11L, -K, H20.035
ReflectionResolution: 1.95→51.778 Å / Num. all: 29944 / Num. obs: 29944 / % possible obs: 71.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.211.90.3152.4786642360.31570.1
2.21-2.351.90.2471.9739339740.24769
2.35-2.511.90.1385.1693137190.13868.9
2.51-2.711.90.17635834180.167.9
2.71-2.971.90.06510.8580831220.06567.9
2.97-3.321.90.04713524328300.04767.7
3.32-3.831.80.03914.4477726410.03971.2
3.83-4.71.80.0318468526520.0384.6
4.7-6.641.90.02720.1411722000.02790.3
6.64-51.7781.90.0329.1216811520.03284.9

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Processing

Software
NameVersionClassificationNB
SCALA3.2.5data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2439 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8034 / SU B: 15.939 / SU ML: 0.196 / SU R Cruickshank DPI: 0.0758 / SU Rfree: 0.0531 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 1512 5.1 %RANDOM
Rwork0.1862 ---
obs0.1892 29894 70.73 %-
all-29894 --
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 max: 123.84 Å2 / Biso mean: 38.3444 Å2 / Biso min: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1--15.22 Å20 Å211.08 Å2
2--24.33 Å20 Å2
3----9.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 23 213 5098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225020
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.9466820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9285630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83823.641217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29915830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2641532
X-RAY DIFFRACTIONr_chiral_restr0.1320.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213785
LS refinement shellResolution: 2.096→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 118 -
Rwork0.215 1843 -
all-1961 -
obs--64.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.1946-1.6383-1.19752.76431.06661.6-0.1841-0.22360.06120.29960.26460.29010.03770.0201-0.08060.11270.050.02420.04340.05870.2671-8.4269.69912.347
23.0176-0.3005-1.40533.68540.29592.2917-0.29240.0372-0.3115-0.29130.1618-0.3690.27760.18060.13060.1364-0.0010.0390.0634-0.0350.283317.95-13.936-10.499
320.7439-12.2833-5.945610.96714.09821.7999-0.6712-0.1839-1.88110.49240.15711.03980.24930.05940.51410.42520.0070.15690.00640.05440.5766-1.64-18.25.229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 370
2X-RAY DIFFRACTION2A396 - 633
3X-RAY DIFFRACTION3A371 - 395

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