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- PDB-4xmi: Crystal structure of the K499G mutant of NanB sialidase from Stre... -

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Basic information

Entry
Database: PDB / ID: 4xmi
TitleCrystal structure of the K499G mutant of NanB sialidase from Streptococcus pneumoniae
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
PHOSPHATE ION / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 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 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 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)74,0118
Polymers73,4481
Non-polymers5647
Water13,223734
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint6 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.295, 82.651, 117.152
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: 73447.719 Da / Num. of mol.: 1 / Fragment: UNP residues 39-696 / Mutation: K499G D643G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
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.: 6 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / 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: 51.08 %
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: Aug 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 52883 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 17.86 Å2 / Rmerge(I) obs: 0.101 / Χ2: 3.145 / Net I/av σ(I): 27.855 / Net I/σ(I): 13 / Num. measured all: 250563
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.97-24.60.2777.926011.994100
2-2.044.70.25625922.2100
2.04-2.084.70.2326382.216100
2.08-2.124.70.22226272.286100
2.12-2.174.70.19926052.351100
2.17-2.224.70.18526082.432100
2.22-2.274.70.17626312.739100
2.27-2.344.80.16926292.702100
2.34-2.44.80.15926152.6100
2.4-2.484.80.15126342.869100
2.48-2.574.80.14226582.837100
2.57-2.674.80.13226513.176100
2.67-2.794.80.12326403.154100
2.79-2.944.80.11326553.417100
2.94-3.134.60.09626443.65699.9
3.13-3.374.40.08626444.03999.5
3.37-3.714.90.07926734.61299.7
3.71-4.244.90.07326884.89699.2
4.24-5.344.90.06526954.55299
5.34-304.70.06327553.9195.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2vw0


Resolution: 1.97→23.8 Å / FOM work R set: 0.8746 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 2601 4.92 %
Rwork0.1645 50227 -
obs0.1666 52828 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.02 Å2 / Biso mean: 17.67 Å2 / Biso min: 3.35 Å2
Refinement stepCycle: final / Resolution: 1.97→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5180 0 29 734 5943
Biso mean--24.47 25.67 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075331
X-RAY DIFFRACTIONf_angle_d1.1037210
X-RAY DIFFRACTIONf_chiral_restr0.079783
X-RAY DIFFRACTIONf_plane_restr0.004931
X-RAY DIFFRACTIONf_dihedral_angle_d14.0361951
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 (%)
1.97-2.00580.22171420.16762582272499
2.0058-2.04440.22351070.167326332740100
2.0444-2.08610.23211620.16125932755100
2.0861-2.13140.19961290.160926112740100
2.1314-2.1810.24331360.166326512787100
2.181-2.23550.27021160.162426142730100
2.2355-2.29590.21611580.162326352793100
2.2959-2.36340.23631390.164225972736100
2.3634-2.43960.23171230.167226592782100
2.4396-2.52670.22661330.166326182751100
2.5267-2.62770.19691380.167126502788100
2.6277-2.74720.21841520.1726422794100
2.7472-2.89180.20421380.171426342772100
2.8918-3.07260.19811570.170626332790100
3.0726-3.30930.18751300.164226832813100
3.3093-3.64120.19981380.160626532791100
3.6412-4.16570.20191430.153326802823100
4.1657-5.23910.15361250.14822694281999
5.2391-23.80180.21161350.19072765290097

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