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

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Basic information

Entry
Database: PDB / ID: 4xja
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 5-acetamido-2,3-difluoro-3-hydroxy-6-[1,2,3-trihydroxypropyl]oxane-2-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-OPX / PHOSPHATE ION / Chem-SFJ / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 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 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 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 3.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3946
Polymers73,5201
Non-polymers8745
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint1 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.586, 82.556, 116.654
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

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sialidase B / Neuraminidase B


Mass: 73519.852 Da / Num. of mol.: 1 / 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
#5: Sugar ChemComp-SFJ / (2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid / (2R,3R,4R,5R,6R)-5-(acetylamino)-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxy lic acid / 2,3-difluoro-sialic acid / 5-acetamido-2,3-difluoro-3-hydroxy-6-[1,2,3-trihydroxypropyl]oxane-2-carboxylic acid


Type: D-saccharide / Mass: 329.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17F2NO8

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Non-polymers , 4 types, 580 molecules

#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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
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: 1.54 Å
DetectorType: RIGAKU / Detector: CCD / Date: May 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.94→20 Å / Num. obs: 54930 / % possible obs: 99.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 19.48 Å2 / Rmerge(I) obs: 0.081 / Χ2: 2.584 / Net I/av σ(I): 28.824 / Net I/σ(I): 13.7 / Num. measured all: 259611
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.94-1.974.50.28827491.955100
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
PHENIXrefinement
HKL-2000data reduction
PHASER2.1.4phasing
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VW0

2vw0


Resolution: 1.98→20 Å / FOM work R set: 0.8768 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 2538 4.92 %
Rwork0.1672 49098 -
obs0.1689 51636 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.68 Å2 / Biso mean: 24.84 Å2 / Biso min: 9.75 Å2
Refinement stepCycle: final / Resolution: 1.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 54 576 5815
Biso mean--23.44 30.99 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075380
X-RAY DIFFRACTIONf_angle_d1.1227288
X-RAY DIFFRACTIONf_chiral_restr0.082791
X-RAY DIFFRACTIONf_plane_restr0.004937
X-RAY DIFFRACTIONf_dihedral_angle_d16.031985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9804-2.01850.20211260.16192670279698
2.0185-2.05970.21571310.164927182849100
2.0597-2.10440.22281570.165526712828100
2.1044-2.15340.22211380.165327322870100
2.1534-2.20720.22891310.166427372868100
2.2072-2.26680.23071410.163527072848100
2.2668-2.33340.21651580.16927072865100
2.3334-2.40870.23521170.170427662883100
2.4087-2.49470.20561480.164827332881100
2.4947-2.59440.2191440.176427152859100
2.5944-2.71230.20951550.171627082863100
2.7123-2.8550.22061350.180127602895100
2.855-3.03350.20391620.17927212883100
3.0335-3.26710.20011410.16942721286299
3.2671-3.59480.17421420.16032749289199
3.5948-4.11230.18771390.15942746288598
4.1123-5.1710.15441310.14622755288697
5.171-22.74550.20881420.19142782292495

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