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- PDB-7a54: Two copies of the catalytic domain of NanA sialidase from Strepto... -

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Basic information

Entry
Database: PDB / ID: 7a54
TitleTwo copies of the catalytic domain of NanA sialidase from Streptococcus pneumoniae juxtaposed in the P212121 space group, in complex with DANA
ComponentsSialidase A
KeywordsSTRUCTURAL PROTEIN / Sialidase / Catalytic domain / DANA
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. / LPXTG cell wall anchor domain / Sialidase superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Sialidase A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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, Y. / Assailly, C. / Saumonneau, A. / Bouckaert, J. / Maillasson, M. / Petitot, C. / Roubinet, B. / Didak, B. / Landemarre, L. / Bridot, C. / Blossey, R. / Deniaud, D. / Yan, X. / ...Authors: Brissonnet, Y. / Assailly, C. / Saumonneau, A. / Bouckaert, J. / Maillasson, M. / Petitot, C. / Roubinet, B. / Didak, B. / Landemarre, L. / Bridot, C. / Blossey, R. / Deniaud, D. / Yan, X. / Bernard, J. / Tellier, C. / Grandjean, C. / Daligault, F. / Gouin, S.G.
History
DepositionAug 20, 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)112,8664
Polymers112,2832
Non-polymers5832
Water4,738263
1
A: Sialidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4332
Polymers56,1421
Non-polymers2911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4332
Polymers56,1421
Non-polymers2911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.870, 96.194, 220.602
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

#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
#2: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.81 % / Description: Beam
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 15% w/v Jeffamine ED 2003, 10% v/v ethanol

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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: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.28→48.1 Å / Num. obs: 31218 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 68.757 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.205 / Net I/σ(I): 9.06
Reflection shellResolution: 2.28→2.42 Å / Redundancy: 11.14 % / Rmerge(I) obs: 0.3775 / Mean I/σ(I) obs: 0.41 / Num. unique obs: 7560 / CC1/2: 0.384 / Rrim(I) all: 0.3954 / % possible all: 93.5

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Processing

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

2ya5


Resolution: 2.7→35.27 Å / SU ML: 0.3182 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2261
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 1244 3.98 %Random selection
Rwork0.206 29972 --
obs0.2076 31218 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.6 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7461 0 40 264 7765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00557663
X-RAY DIFFRACTIONf_angle_d0.775610352
X-RAY DIFFRACTIONf_chiral_restr0.05171094
X-RAY DIFFRACTIONf_plane_restr0.00361351
X-RAY DIFFRACTIONf_dihedral_angle_d15.26332863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.810.31881350.3123270X-RAY DIFFRACTION99.91
2.81-2.940.30221370.3023272X-RAY DIFFRACTION99.91
2.94-3.090.36251350.29563272X-RAY DIFFRACTION99.85
3.09-3.280.37951380.29123291X-RAY DIFFRACTION99.94
3.28-3.540.33541360.25473305X-RAY DIFFRACTION99.77
3.54-3.890.28151370.22633302X-RAY DIFFRACTION99.85
3.89-4.460.18841390.16423327X-RAY DIFFRACTION99.86
4.46-5.610.17371400.15213385X-RAY DIFFRACTION100
5.61-35.270.21791470.18133548X-RAY DIFFRACTION99.73

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