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- PDB-2fhr: Trypanosoma Rangeli Sialidase In Complex With 2,3- Difluorosialic... -

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Basic information

Entry
Database: PDB / ID: 2fhr
TitleTrypanosoma Rangeli Sialidase In Complex With 2,3- Difluorosialic Acid (Covalent Intermediate)
Componentssialidase
KeywordsHYDROLASE / BETA-PROPELLER / COVALENT ENZYME-INTERMEDIATE COMPLEX / BETA-SANDWICH
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / : / : / : / exo-alpha-sialidase / 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 / Neuraminidase ...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
Chem-FSI / : / Sialidase
Similarity search - Component
Biological speciesTrypanosoma rangeli (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 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
DepositionDec 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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.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 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)71,8175
Polymers71,2051
Non-polymers6114
Water6,990388
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.873, 95.007, 110.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer and corresponds to the monomer present in the ASU

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Components

#1: Protein sialidase


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: GenBank: 2894810, UniProt: O44049*PLUS, 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-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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 291 K / pH: 6.5
Details: PEG 8000, AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979158
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: 2.2→72.17 Å / Num. obs: 36222 / % possible obs: 89.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / Rsym value: 0.34 / % possible all: 90.8

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→29.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.365 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.212 / Stereochemistry target values: ENGH & HUBER
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TLS PARAMETERS HAVE BEEN REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1817 5.021 %RANDOM
Rwork0.16 ---
obs0.164 36190 88.8 %-
all-36190 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 28.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.648 Å20 Å20 Å2
2---1.065 Å20 Å2
3----1.584 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 37 388 5247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225018
X-RAY DIFFRACTIONr_bond_other_d0.0010.024499
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.9486828
X-RAY DIFFRACTIONr_angle_other_deg0.895310436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8475633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7723.484221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22815811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9351538
X-RAY DIFFRACTIONr_chiral_restr0.110.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025647
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021048
X-RAY DIFFRACTIONr_nbd_refined0.2080.2947
X-RAY DIFFRACTIONr_nbd_other0.1950.24615
X-RAY DIFFRACTIONr_nbtor_refined0.180.22413
X-RAY DIFFRACTIONr_nbtor_other0.0890.23020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2386
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0520.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2461.53947
X-RAY DIFFRACTIONr_mcbond_other0.2641.51296
X-RAY DIFFRACTIONr_mcangle_it1.56625036
X-RAY DIFFRACTIONr_scbond_it2.40932249
X-RAY DIFFRACTIONr_scangle_it3.4284.51791
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 140 -
Rwork0.203 2523 -
obs--90.45 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3379-0.07030.00340.42370.07360.2876-0.00630.003700.04160.0396-0.01430.08470.0312-0.0332-0.01570.01740.0022-0.029-0.0073-0.034547.295-4.54155.048
20.5539-0.36070.16970.7952-0.22320.32090.03640.01790.0319-0.0861-0.0507-0.01320.0347-0.00940.0144-0.0403-0.01850.0067-0.01190.0066-0.033820.82422.46436.112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 37214 - 386
2X-RAY DIFFRACTION2AA422 - 631436 - 645

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