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- PDB-4xil: Crystal structure of the NanB sialidase from streptococcus pneumo... -

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Basic information

Entry
Database: PDB / ID: 4xil
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with Optactin at pH 7.4 in PBS with MPD as the cryoprotectant
ComponentsSialidase B
KeywordsHYDROLASE / intramolecular trans-sialidase / glycosidase / drug design / neuraminidase / allosteric inhibitor / serendipitous allosteric sites / crystallization artefacts
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
BNR repeat / BNR/Asp-box repeat / Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase ...BNR repeat / BNR/Asp-box repeat / Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / 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 / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-OPX / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBrear, P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
SULSA United Kingdom
CitationJournal: To be published
Title: `The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB
Authors: Rogers, G.W. / Brear, P. / Yang, L. / Chen, A.S. / Mitchell, J.B.O. / Taylor, G.L. / Westwood, N.J.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 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

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Assembly

Deposited unit
A: Sialidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8132
Polymers73,5201
Non-polymers2931
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.528, 82.837, 117.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Sialidase B / Neuraminidase B


Mass: 73519.852 Da / Num. of mol.: 1 / Fragment: UNP residues 39-696 / Mutation: D643G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: nanB, SP_1687 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical ChemComp-OPX / (1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid


Mass: 293.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H23NO5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 7% PEG 8000, 0.1M IMIDAZOLE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Oct 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 55167 / % possible obs: 92.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.72 Å2 / Rmerge(I) obs: 0.091 / Χ2: 3.434 / Net I/av σ(I): 30.912 / Net I/σ(I): 14.3 / Num. measured all: 244587
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.934.50.28329192.12399.5
1.93-1.974.50.2529622.28499.8
1.97-2.014.50.23129062.42899.8
2.01-2.054.50.20829232.5999.8
2.05-2.094.50.1929542.65899.9
2.09-2.144.60.16829412.713100
2.14-2.194.60.15429502.814100
2.19-2.254.60.14329492.93100
2.25-2.324.60.13529373.15100
2.32-2.394.70.12729873.207100
2.39-2.484.70.11929353.447100
2.48-2.584.70.11329593.699100
2.58-2.74.70.10629493.8499.9
2.7-2.844.70.09929914.05999.6
2.84-3.023.90.08827134.11291.3
3.02-3.251.70.076023.1120.1
3.25-3.573.40.07818545.99561.6
3.57-4.094.20.06828415.79593.9
4.09-5.153.90.05728055.33591.5
5.15-304.50.05530904.29496.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.22 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.42 Å
Translation2.5 Å27.42 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VW0

2vw0


Resolution: 1.9→27.416 Å / FOM work R set: 0.8778 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 2713 4.92 %
Rwork0.1606 52391 -
obs0.1624 55104 92.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.3 Å2 / Biso mean: 19.28 Å2 / Biso min: 5.77 Å2
Refinement stepCycle: final / Resolution: 1.9→27.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 19 544 5748
Biso mean--15.1 24.09 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075330
X-RAY DIFFRACTIONf_angle_d1.0817215
X-RAY DIFFRACTIONf_chiral_restr0.079784
X-RAY DIFFRACTIONf_plane_restr0.004930
X-RAY DIFFRACTIONf_dihedral_angle_d14.2971971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93450.22221540.17932929308399
1.9345-1.97170.22071430.16829423085100
1.9717-2.0120.22041590.167929223081100
2.012-2.05570.19231300.162629583088100
2.0557-2.10350.21561690.156228963065100
2.1035-2.15610.20661470.160529593106100
2.1561-2.21440.2281440.155129643108100
2.2144-2.27950.20141530.158729343087100
2.2795-2.3530.20321690.165729613130100
2.353-2.43710.21221340.16929763110100
2.4371-2.53460.2191560.172529473103100
2.5346-2.64990.22251560.169429593115100
2.6499-2.78940.2191610.173329473108100
2.7894-2.9640.21131760.18082890306697
2.964-3.19260.2334560.18331123117938
3.1926-3.51330.2134700.17171351142145
3.5133-4.02030.17811460.15172894304096
4.0203-5.05990.14121350.13292752288790
5.0599-27.41880.17641550.15383087324297

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