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- PDB-4xio: Crystal structure of apo NanB sialidase from streptococcus pneumo... -

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Basic information

Entry
Database: PDB / ID: 4xio
TitleCrystal structure of apo NanB sialidase from streptococcus pneumoniae at pH 8.0 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
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms
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 / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance
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


Theoretical massNumber of molelcules
Total (without water)73,5201
Polymers73,5201
Non-polymers00
Water15,475859
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.481, 82.738, 117.547
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 51.37 %
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: 1.8→30 Å / Num. obs: 68995 / % possible obs: 98.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.22 Å2 / Rmerge(I) obs: 0.058 / Χ2: 2.246 / Net I/av σ(I): 33.079 / Net I/σ(I): 18.1 / Num. measured all: 299011
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.832.60.23931812.08392
1.83-1.8630.21733612.14497.8
1.86-1.93.80.22234102.24399.1
1.9-1.944.20.19334592.31999.9
1.94-1.984.30.15134452.15499.9
1.98-2.034.40.1334692.217100
2.03-2.084.40.11534432.252100
2.08-2.134.40.10934542.32499.9
2.13-2.24.40.09934622.274100
2.2-2.274.40.09234732.29799.9
2.27-2.354.40.08834592.26699.9
2.35-2.444.40.08234812.23899.8
2.44-2.554.50.07634822.2799.9
2.55-2.694.50.07234842.24899.9
2.69-2.864.60.06435032.26199.9
2.86-3.084.70.05434942.25999.8
3.08-3.394.80.04535132.27799.6
3.39-3.884.80.03935052.41199
3.88-4.884.80.03334772.05297.1
4.88-304.90.03234402.18991.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.56 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å21.37 Å
Translation2.5 Å21.37 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: 1.8→21.369 Å / FOM work R set: 0.8694 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 3422 4.97 %
Rwork0.1613 65410 -
obs0.1631 68832 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.93 Å2 / Biso mean: 15.35 Å2 / Biso min: 2.44 Å2
Refinement stepCycle: final / Resolution: 1.8→21.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 0 859 6044
Biso mean---24.39 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075341
X-RAY DIFFRACTIONf_angle_d1.0987236
X-RAY DIFFRACTIONf_chiral_restr0.08790
X-RAY DIFFRACTIONf_plane_restr0.004938
X-RAY DIFFRACTIONf_dihedral_angle_d13.5091971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7995-1.82520.2851650.23122467263291
1.8252-1.85240.28541400.20962620276097
1.8524-1.88130.28481350.20652694282999
1.8813-1.91220.23171360.200727422878100
1.9122-1.94510.23221410.179626942835100
1.9451-1.98050.2411350.185827412876100
1.9805-2.01850.20651390.175727522891100
2.0185-2.05970.19831340.152927372871100
2.0597-2.10440.18811580.149626952853100
2.1044-2.15340.19111410.151427452886100
2.1534-2.20720.21271310.155327632894100
2.2072-2.26680.20861410.159727512892100
2.2668-2.33340.231590.169427282887100
2.3334-2.40860.23231260.173127472873100
2.4086-2.49460.23011450.173727562901100
2.4946-2.59430.21581400.176727532893100
2.5943-2.71210.20341570.168927452902100
2.7121-2.85480.19741330.17342763289699
2.8548-3.03320.20361660.17632716288299
3.0332-3.26660.19221450.16172767291299
3.2666-3.5940.17241400.14222777291799
3.594-4.11080.15311420.13432772291499
4.1108-5.16710.14641310.13282747287896
5.1671-21.37020.17351420.15782738288092

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