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

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Basic information

Entry
Database: PDB / ID: 4fpf
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 2-[(3-Chlorobenzyl)ammonio]ethanesulfonate
ComponentsSialidase B
KeywordsHYDROLASE/INHIBITOR / hydrolase / intramolecular trans-sialidase / glycosidase / drug design / neuraminidase / HYDROLASE-INHIBITOR complex
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
2-[(3-chlorobenzyl)amino]ethanesulfonic acid / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsBrear, P.
CitationJournal: Chembiochem / Year: 2012
Title: Synthesis and structural characterisation of selective non-carbohydrate-based inhibitors of bacterial sialidases.
Authors: Brear, P. / Telford, J. / Taylor, G.L. / Westwood, N.J.
History
DepositionJun 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)78,1874
Polymers77,7811
Non-polymers4063
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.376, 82.579, 116.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sialidase B / Neuraminidase B


Mass: 77780.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: nanB, SP_1687 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical ChemComp-JKK / 2-[(3-chlorobenzyl)amino]ethanesulfonic acid


Mass: 249.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12ClNO3S
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 7% PEG 8000, 0.1M IMIDAZOLE, pH 8.0, vapor diffusion, sitting drop, temperature 298K

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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 SATURN 944 / Detector: CCD / Date: Mar 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→40 Å / Num. obs: 36722 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.104 / Χ2: 2.828 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.23-2.273.50.29817742.305199.1
2.27-2.314.20.31818332.2199.8
2.31-2.354.60.28918082.246199.9
2.35-2.44.60.28517932.168199.7
2.4-2.454.60.25318192.338199.9
2.45-2.514.60.24518202.374199.9
2.51-2.574.70.22418202.3221100
2.57-2.644.70.20318122.462199.9
2.64-2.724.70.18818192.449199.9
2.72-2.814.70.17218242.5871100
2.81-2.914.80.15518272.671100
2.91-3.034.80.13718232.845199.9
3.03-3.164.80.1218523.0071100
3.16-3.334.80.10118433.1941100
3.33-3.544.80.09318123.454199.9
3.54-3.814.80.0818673.5951100
3.81-4.24.80.07518533.7311100
4.2-4.84.80.06618833.778199.9
4.8-6.054.80.06518843.177199.6
6.05-404.60.05619563.13197

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.03 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.88 Å
Translation2.5 Å25.88 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→25.877 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1827 4.98 %RANDOM
Rwork0.1736 ---
obs0.1762 36662 99.64 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.759 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 87.72 Å2 / Biso mean: 25.4658 Å2 / Biso min: 9.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.2426 Å2-0 Å20 Å2
2---1.8509 Å2-0 Å2
3---8.0935 Å2
Refinement stepCycle: LAST / Resolution: 2.23→25.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 23 580 5792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075374
X-RAY DIFFRACTIONf_angle_d1.077282
X-RAY DIFFRACTIONf_chiral_restr0.076794
X-RAY DIFFRACTIONf_plane_restr0.004941
X-RAY DIFFRACTIONf_dihedral_angle_d13.4871985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.28720.27541530.17622569272297
2.2872-2.35450.29621390.194526372776100
2.3545-2.43040.24571200.185426642784100
2.4304-2.51720.29411410.181526422783100
2.5172-2.61790.23061370.173326692806100
2.6179-2.7370.23581490.167626602809100
2.737-2.88110.22481440.172626632807100
2.8811-3.06130.23241580.17126602818100
3.0613-3.29730.22471350.172826822817100
3.2973-3.62830.22561380.167726952833100
3.6283-4.15140.2061430.169927122855100
4.1514-5.22330.181290.150227442873100
5.2233-25.8770.20861410.20222838297999

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