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- PDB-1mz6: Trypanosoma rangeli sialidase in complex with the inhibitor DANA -

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Basic information

Entry
Database: PDB / ID: 1mz6
TitleTrypanosoma rangeli sialidase in complex with the inhibitor DANA
Componentssialidase
Keywordshydrolase / hydrolase inhibitor / inibitor complex / trypanosomal sialidase / sialyltransferase
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: 2.9 Å
AuthorsBuschiazzo, A. / Tavares, G.A. / Campetella, O. / Spinelli, S. / Cremona, M.L. / Paris, G. / Amaya, M.F. / Frasch, A.C.C. / Alzari, P.M.
CitationJournal: 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.C. / Alzari, P.M.
History
DepositionOct 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 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

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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)71,1037
Polymers69,7051
Non-polymers1,3976
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.200, 93.800, 105.300
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


Mass: 69705.445 Da / Num. of mol.: 1 / Fragment: mature sialidase / Source method: isolated from a natural source / Source: (natural) Trypanosoma rangeli (eukaryote) / References: UniProt: O44049, exo-alpha-sialidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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.: 40 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG-8000, ammonium sulfate, morpholinoethanesulfonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlenzyme1drop
217 %PEG80001reservoir
3100 mMammonium sulfate1reservoir
450 mMMOPS1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. all: 17063 / Num. obs: 17063 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.138
Reflection shellResolution: 2.9→2.98 Å / Rsym value: 0.306 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 112960 / Rmerge(I) obs: 0.138
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.306

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unliganded T. rangeli sialidase 1MZ5

1mz5


Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.776 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28689 869 5.1 %RANDOM
Rwork0.20466 ---
all0.20884 16159 --
obs0.20884 16159 99.26 %-
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: 22.262 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4759 0 90 40 4889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214961
X-RAY DIFFRACTIONr_angle_refined_deg2.3951.9546751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5853617
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.08615828
X-RAY DIFFRACTIONr_chiral_restr0.1430.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023739
X-RAY DIFFRACTIONr_nbd_refined0.2830.32544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5528
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.331
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.51
X-RAY DIFFRACTIONr_mcbond_it0.5941.53065
X-RAY DIFFRACTIONr_mcangle_it1.12124936
X-RAY DIFFRACTIONr_scbond_it1.81831896
X-RAY DIFFRACTIONr_scangle_it3.0414.51815
LS refinement shellResolution: 2.9→2.973 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.367 59
Rwork0.232 1031
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 16275 / Rfactor Rfree: 0.314 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d0.063

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