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- PDB-3b69: T cruzi Trans-sialidase complex with benzoylated NANA derivative -

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Basic information

Entry
Database: PDB / ID: 3b69
TitleT cruzi Trans-sialidase complex with benzoylated NANA derivative
ComponentsTrans-sialidase
KeywordsHYDROLASE / beta-propeller
Function / homology
Function and homology information


exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / intracellular membrane-bounded organelle / membrane / cytoplasm
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
Chem-BFN / Trans-sialidase / Trans-sialidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsBuschiazzo, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2008
Title: A new generation of specific Trypanosoma cruzi trans-sialidase inhibitors.
Authors: Buchini, S. / Buschiazzo, A. / Withers, S.G.
History
DepositionOct 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 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 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE AUTHORS INDICATE THAT THE SEQUENCE IN THE DATABASE IS INCORRECT

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trans-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0934
Polymers71,3891
Non-polymers7043
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.430, 129.200, 54.440
Angle α, β, γ (deg.)90.000, 107.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trans-sialidase


Mass: 71389.258 Da / Num. of mol.: 1 / Mutation: N59F, S496K, V497G, E521K, D594G, I598D, H600R
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): TOP10
References: UniProt: Q26966, UniProt: Q26964*PLUS, exo-alpha-sialidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-BFN / 5-acetamido-9-(benzoylamino)-3,5,9-trideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 5-(acetylamino)-9-(benzoylamino)-3,5,9-trideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 5-acetamido-9-(benzoylamino)-3,5,9-trideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulosonic acid / 5-acetamido-9-(benzoylamino)-3,5,9-trideoxy-3-fluoro-D-erythro-L-manno-non-2-ulosonic acid / 5-acetamido-9-(benzoylamino)-3,5,9-trideoxy-3-fluoro-D-erythro-manno-non-2-ulosonic acid


Type: D-saccharide, beta linking / Mass: 430.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23FN2O9
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG4000, 5% isopropanol, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 8, 2007 / Details: VarimaxHF mirrors
RadiationMonochromator: confocal multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: l,-k,h / Fraction: 0.33
ReflectionResolution: 1.67→64.599 Å / Num. all: 76475 / Num. obs: 76475 / % possible obs: 91.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.67-1.762.10.2453.11938791100.24574.6
1.76-1.862.10.1574.821515103420.15790.5
1.86-1.9920.1017.320662100870.10193.7
1.99-2.152.10.06311.51985596330.06395.6
2.15-2.362.10.04715.11905889370.04796.5
2.36-2.632.20.03618.81795681540.03697.6
2.63-3.042.30.02823.71650672940.02898.3
3.04-3.732.30.02327.61401961490.02398.3
3.73-5.272.20.02321007045280.0293.3
5.27-20.842.20.0233.4504122410.0283.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.356 / Cor.coef. Fo:Fc: 0.631 / Cor.coef. Io to Ic: 0.601
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AH2

2ah2


Resolution: 1.67→50 Å / Isotropic thermal model: restrained isotropic / Cross valid method: THROUGHOUT / σ(F): 3334 / Stereochemistry target values: Engh & Huber
Details: Refinement was performed with the least squares target for hemihedrally twinned structures, as implemented in CNS v1.2 (twin operator l,-k,h; twin fraction 0.33)
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2149 2.6 %random, the twin operator (l,-k,h) was taken into account to keep the same test flag for the twin pairs
Rwork0.147 ---
all0.147 76475 --
obs0.147 73113 88.2 %-
Solvent computationBsol: 52.03 Å2
Displacement parametersBiso mean: 26.606 Å2
Baniso -1Baniso -2Baniso -3
1--1.021 Å20 Å24.853 Å2
2---3.036 Å20 Å2
3---4.057 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.67→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4883 0 60 378 5321
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_scbond_it1.6722
X-RAY DIFFRACTIONc_mcangle_it1.8512
X-RAY DIFFRACTIONc_scangle_it2.4262.5
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.71213
X-RAY DIFFRACTIONc_dihedral_angle_deg25.75673
X-RAY DIFFRACTIONc_improper_angle_deg0.98166
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2bfn.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5hepes2.param

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