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- PDB-2a75: Trypanosoma rangeli Sialidase In Complex With 2,3- Difluorosialic... -

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Basic information

Entry
Database: PDB / ID: 2a75
TitleTrypanosoma rangeli Sialidase In Complex With 2,3- Difluorosialic Acid (Covalent Intermediate)
ComponentssialidaseNeuraminidase
KeywordsHYDROLASE / beta-propeller / covalent enzyme-intermediate complex / beta-sandwich
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / metabolic process
Similarity search - Function
Trypanosome sialidase / BNR repeat-like domain / Concanavalin A-like lectin/glucanases superfamily / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 ...Trypanosome sialidase / BNR repeat-like domain / Concanavalin A-like lectin/glucanases superfamily / 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-FSI / Sialidase
Similarity search - Component
Biological speciesTrypanosoma rangeli (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsAmaya, M.F. / Alzari, P.M. / Buschiazzo, A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and Kinetic Analysis of Two Covalent Sialosyl-Enzyme Intermediates on Trypanosoma rangeli Sialidase.
Authors: Watts, A.G. / Oppezzo, P. / Withers, S.G. / Alzari, P.M. / Buschiazzo, A.
History
DepositionJul 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jul 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _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 1.5Aug 23, 2023Group: 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_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN The covalent Sialo-Tyrosine adduct is the product of the reaction of 2,3-difluorosialic ...HETEROGEN The covalent Sialo-Tyrosine adduct is the product of the reaction of 2,3-difluorosialic acid with the enzyme
Remark 999SEQUENCE Authors indicate 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: sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7254
Polymers71,2051
Non-polymers5193
Water11,079615
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.218, 96.102, 106.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer

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Components

#1: Protein sialidase / Neuraminidase


Mass: 71205.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma rangeli (eukaryote) / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O44049, exo-alpha-sialidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-FSI / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid / 3-FLUOROSIALIC ACID / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-L-manno-non-2-ulosonic acid / 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-manno-non-2-ulosonic acid


Type: D-saccharide, beta linking / Mass: 327.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H18FNO9
IdentifierTypeProgram
b-D-Neup5Ac3fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979158 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2003
RadiationMonochromator: Si 311 channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979158 Å / Relative weight: 1
ReflectionResolution: 1.9→46.63 Å / Num. all: 47608 / Num. obs: 47608 / % possible obs: 91.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 3.9
Reflection shellResolution: 1.9→2 Å / % possible obs: 80.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.7 / Num. measured obs: 6972 / Num. unique all: 6972 / Rsym value: 0.3 / % possible all: 80.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1N1S

1n1s


Resolution: 1.95→29.04 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2413 5.1 %RANDOM
Rwork0.174 ---
all0.174 55967 --
obs0.174 47602 85.1 %-
Solvent computationSolvent model: CNS bulk solvent model / Bsol: 46.1351 Å2 / ksol: 0.364945 e/Å3
Displacement parametersBiso max: 56.5 Å2 / Biso mean: 11.58 Å2 / Biso min: 1.36 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å20 Å20 Å2
2---0.51 Å20 Å2
3----2.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.03 Å
Luzzati d res high-1.95
Refinement stepCycle: LAST / Resolution: 1.95→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 31 615 5564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONx_scbond_it2.182
X-RAY DIFFRACTIONx_scangle_it3.032.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.95-2.040.24429250.20255460.0146929583884.3
2.04-2.150.2313305.50.17356640.0136916599486.7
2.15-2.280.2061184.80.15523160.0196926243435.1
2.28-2.460.20328050.15453110.0126942559180.5
2.46-2.710.2133094.70.15462810.0126964659094.6
2.71-3.10.213655.30.16365330.0117005689898.5
3.1-3.90.2253615.10.19466750.0127046703699.9
3.9-29.040.20335850.17468630.0117292722199

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