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- PDB-7a5x: Two copies of the catalytic domain of NanA sialidase from Strepto... -

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Basic information

Entry
Database: PDB / ID: 7a5x
TitleTwo copies of the catalytic domain of NanA sialidase from Streptococcus pneumoniae juxtaposed in the P212121 space group, in complex with DANA derivatized with a PEG linker on the glycerol group.
ComponentsSialidase A
KeywordsSTRUCTURAL PROTEIN / Sialidase / Catalytic domain / CA170
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm
Similarity search - Function
: / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family / Sialidase / YSIRK type signal peptide ...: / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family / Sialidase / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Gram-positive cocci surface proteins LPxTG motif profile. / Sialidase superfamily / LPXTG cell wall anchor domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-R7H / Sialidase A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsBridot, C. / Bouckaert, J.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE07-0028-03 France
Citation
Journal: Chemistry / Year: 2021
Title: Polyvalent Transition-State Analogues of Sialyl Substrates Strongly Inhibit Bacterial Sialidases*.
Authors: Assailly, C. / Bridot, C. / Saumonneau, A. / Lottin, P. / Roubinet, B. / Krammer, E.M. / Francois, F. / Vena, F. / Landemarre, L. / Alvarez Dorta, D. / Deniaud, D. / Grandjean, C. / Tellier, ...Authors: Assailly, C. / Bridot, C. / Saumonneau, A. / Lottin, P. / Roubinet, B. / Krammer, E.M. / Francois, F. / Vena, F. / Landemarre, L. / Alvarez Dorta, D. / Deniaud, D. / Grandjean, C. / Tellier, C. / Pascual, S. / Montembault, V. / Fontaine, L. / Daligault, F. / Bouckaert, J. / Gouin, S.G.
#1: Journal: Chemistry / Year: 2019
Title: Multivalent Thiosialosides and Their Synergistic Interaction with Pathogenic Sialidases.
Authors: Brissonnet, J.
History
DepositionAug 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 A
B: Sialidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,62212
Polymers112,2832
Non-polymers1,33910
Water13,439746
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-87 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.203, 96.741, 226.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sialidase A / Neuraminidase A


Mass: 56141.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: nanA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62575, exo-alpha-sialidase

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Non-polymers , 5 types, 756 molecules

#2: Chemical ChemComp-R7H / (4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{S})-3-[[1-(2-ethoxyethyl)-1,2,3-triazol-4-yl]methylsulfanyl]-1,2-bis(oxidanyl)propyl]-4-oxidanyl-oxane-2-carboxylic acid


Mass: 462.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H30N4O8S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Ammonium sulfate, 0.1M Tris pH=8,5 35% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.94→56.6 Å / Num. obs: 80186 / % possible obs: 99.3 % / Redundancy: 8.43 % / Biso Wilson estimate: 38.564 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.171 / Net I/σ(I): 10.02
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.1628 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 12318 / CC1/2: 0.477 / Rrim(I) all: 0.1731 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660model building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YA5

2ya5


Resolution: 1.94→56.6 Å / SU ML: 0.2973 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 4008 5 %
Rwork0.1888 76146 -
obs0.1912 80154 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.6 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.38 Å2
Refinement stepCycle: LAST / Resolution: 1.94→56.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7523 0 16 746 8285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157747
X-RAY DIFFRACTIONf_angle_d1.346110470
X-RAY DIFFRACTIONf_chiral_restr0.07181101
X-RAY DIFFRACTIONf_plane_restr0.00911365
X-RAY DIFFRACTIONf_dihedral_angle_d16.83332909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.970.3781080.33352073X-RAY DIFFRACTION79.14
1.97-1.990.35491360.31682570X-RAY DIFFRACTION100
1.99-2.020.38761370.29392609X-RAY DIFFRACTION99.93
2.02-2.040.32281380.2812617X-RAY DIFFRACTION100
2.04-2.070.3291370.27382603X-RAY DIFFRACTION99.96
2.07-2.10.28511370.25342605X-RAY DIFFRACTION99.93
2.1-2.130.29151380.26712630X-RAY DIFFRACTION99.96
2.13-2.160.34561370.26452593X-RAY DIFFRACTION99.93
2.16-2.20.29391370.25172598X-RAY DIFFRACTION100
2.2-2.240.31551400.25642656X-RAY DIFFRACTION100
2.24-2.280.2811350.25672568X-RAY DIFFRACTION99.96
2.28-2.320.29051390.25042651X-RAY DIFFRACTION99.96
2.32-2.370.33491380.25982621X-RAY DIFFRACTION99.96
2.37-2.420.33641380.25362619X-RAY DIFFRACTION100
2.42-2.480.27581390.25032637X-RAY DIFFRACTION99.96
2.48-2.540.30931360.23922585X-RAY DIFFRACTION99.93
2.54-2.610.28221400.2172662X-RAY DIFFRACTION100
2.61-2.680.27081380.2082610X-RAY DIFFRACTION100
2.68-2.770.29521390.20222654X-RAY DIFFRACTION100
2.77-2.870.25671400.19182647X-RAY DIFFRACTION100
2.87-2.990.23841380.1872625X-RAY DIFFRACTION100
2.99-3.120.24961410.18272678X-RAY DIFFRACTION100
3.12-3.290.23691410.17312678X-RAY DIFFRACTION100
3.29-3.490.21541390.16152649X-RAY DIFFRACTION100
3.49-3.760.20551410.16162676X-RAY DIFFRACTION100
3.76-4.140.17071410.14282692X-RAY DIFFRACTION100
4.14-4.740.17631430.12652702X-RAY DIFFRACTION100
4.74-5.970.17411440.13992743X-RAY DIFFRACTION99.97
5.97-56.60.20091530.18042895X-RAY DIFFRACTION99.74

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