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

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Basic information

Entry
Database: PDB / ID: 4xju
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 4-acetamido-2-fluoro-3-hydroxy-6-[1,2-dihydroxyethyl]-7,8-dioxabicyclo[3.2.1]octane-1-carboxylic acid
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-19D / PHOSPHATE ION / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 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 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / 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 / _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)74,2377
Polymers73,5201
Non-polymers7176
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint4 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.414, 82.418, 116.697
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 serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: nanB, SP_1687 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-19D / (1R,2R,3R,4R,5R,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-4-fluoro-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid


Mass: 309.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16FNO8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
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: May 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→20 Å / Num. obs: 56319 / % possible obs: 98.97 % / Redundancy: 4.6 % / Biso Wilson estimate: 18.71 Å2 / Rmerge(I) obs: 0.084 / Χ2: 2.584 / Net I/av σ(I): 28.824 / Net I/σ(I): 34.7 / Num. measured all: 259611
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.92-1.954.60.249.927491.955100
1.97-2.014.50.25427251.978100
2.01-2.054.60.22927222.039100
2.05-2.094.60.21427162.131100
2.09-2.144.60.19627402.19899.9
2.14-2.184.70.17827352.22899.9
2.18-2.244.70.16127172.296100
2.24-2.34.70.15227592.3899.9
2.3-2.374.70.14327242.40299.9
2.37-2.444.70.13327522.399100
2.44-2.534.70.12727492.51999.9
2.53-2.634.80.11827472.54799.8
2.63-2.754.80.10627662.58699.7
2.75-2.94.80.09427292.74799.5
2.9-3.084.80.08127552.88499.2
3.08-3.314.80.06927693.03699.1
3.31-3.644.90.05727523.07898.4
3.64-4.174.90.05327473.29198
4.17-5.244.90.04927533.2797.1
5.24-204.80.05328243.40494.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.43 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.15 Å
Translation2.5 Å29.15 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: 1.94→19.894 Å / FOM work R set: 0.8672 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 2764 4.91 %
Rwork0.1699 53555 -
obs0.1717 56319 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.06 Å2 / Biso mean: 26.03 Å2 / Biso min: 11.54 Å2
Refinement stepCycle: final / Resolution: 1.94→19.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 42 665 5892
Biso mean--32.57 33.02 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075419
X-RAY DIFFRACTIONf_angle_d1.1397353
X-RAY DIFFRACTIONf_chiral_restr0.08796
X-RAY DIFFRACTIONf_plane_restr0.011952
X-RAY DIFFRACTIONf_dihedral_angle_d13.6142024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.95310.23091310.171326572788100
1.9531-1.98860.22831410.173126402781100
1.9886-2.02680.22391150.171527192834100
2.0268-2.06810.24051440.170726732817100
2.0681-2.1130.24891490.168826932842100
2.113-2.16210.20841410.17226522793100
2.1621-2.21610.23131190.163226882807100
2.2161-2.2760.23351530.166926592812100
2.276-2.34280.23211500.172926862836100
2.3428-2.41830.20991150.173926882803100
2.4183-2.50460.25581450.169926942839100
2.5046-2.60470.21251420.178426772819100
2.6047-2.72290.19281470.169726972844100
2.7229-2.86610.1991400.178726952835100
2.8661-3.04510.21341590.185227082867100
3.0451-3.27920.21541340.17722474260892
3.2792-3.60750.19961240.16482445256989
3.6075-4.12540.18781430.160127332876100
4.1254-5.18230.14581290.147728112940100
5.1823-19.8950.19961430.18822866300999

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