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- PDB-1n1t: Trypanosoma rangeli sialidase in complex with DANA at 1.6 A -

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Basic information

Entry
Database: PDB / ID: 1n1t
TitleTrypanosoma rangeli sialidase in complex with DANA at 1.6 A
ComponentsSialidase
KeywordsHYDROLASE / BETA PROPELLER / LECTIN-LIKE FOLD
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
: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / Concanavalin A-like lectin/glucanases superfamily / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller ...: / Trans-sialidase, C-terminal domain / Trypanosome sialidase / Concanavalin A-like lectin/glucanases superfamily / 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
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Sialidase
Similarity search - Component
Biological speciesTrypanosoma rangeli (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAmaya, M.F. / Buschiazzo, A. / Nguyen, T. / Alzari, P.M.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The high resolution structures of free and inhibitor-bound Trypanosoma rangeli sialidase and its comparison with T. cruzi trans-sialidase
Authors: Amaya, M.F. / Buschiazzo, A. / Nguyen, T. / Alzari, P.M.
#1: Journal: Embo J. / Year: 2000
Title: Structural basis of sialyltransferase activity in trypanosomal sialidases
Authors: Buschiazzo, A. / Tavares, G.A. / Campetella, O. / Spinelli, S. / Cremona, M.L. / Paris, G. / Amaya, M.F. / Frasch, A.C. / Alzari, P.M.
History
DepositionOct 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / struct_ref_seq_dif ...chem_comp / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_ref_seq_dif.details / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence The author maintains that the sequence in the sequence database is incorrect

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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)70,3964
Polymers69,9131
Non-polymers4833
Water11,908661
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.945, 96.258, 106.513
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 / 3.2.1.18


Mass: 69912.727 Da / Num. of mol.: 1 / Fragment: residue 23-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma rangeli (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: O44049, exo-alpha-sialidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG-8000, sodium cacodylate, ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMsodium phosphate1drop
330 mMsodium acetate1droppH7.0
416 %(w/w)PEG80001reservoir
550 mMsodium cacodylate1reservoir
6100 mMammonium sulfate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 95328 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.066
Reflection shellResolution: 1.6→1.63 Å / Rsym value: 0.192 / % possible all: 94.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 351240 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 94.4 % / Rmerge(I) obs: 0.192

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N1S

1n1s


Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4771 5 %RANDOM
Rwork0.17303 ---
all0.17424 90373 --
obs0.17424 90373 94.6 %-
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: 14.102 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 30 661 5522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214962
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9416748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3733626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45915849
X-RAY DIFFRACTIONr_chiral_restr0.1230.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023766
X-RAY DIFFRACTIONr_nbd_refined0.2220.32287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.5756
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.330
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.524
X-RAY DIFFRACTIONr_mcbond_it0.9061.53106
X-RAY DIFFRACTIONr_mcangle_it1.63725005
X-RAY DIFFRACTIONr_scbond_it2.48931856
X-RAY DIFFRACTIONr_scangle_it3.9094.51743
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.204 371
Rwork0.178 6560
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.61
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.63 Å

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