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

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Basic information

Entry
Database: PDB / ID: 4fpk
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 2-[(3-methylbenzyl)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-methylbenzyl)amino]ethanesulfonic acid / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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)78,0883
Polymers77,7811
Non-polymers3072
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.231, 82.551, 116.299
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-IJ1 / 2-[(3-methylbenzyl)amino]ethanesulfonic acid


Mass: 229.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO3S
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
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: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 25385 / % possible obs: 86.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Χ2: 3.995 / Net I/σ(I): 26.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.444.70.10314373.634199.4
2.44-2.494.50.10714153.865198.7
2.49-2.534.40.12214005.822198.4
2.53-2.584.60.10114334.015199.2
2.58-2.644.70.09414333.996199.2
2.64-2.74.60.09214324.072199.7
2.7-2.774.50.09114144.115198
2.77-2.844.20.08314163.936196.1
2.84-2.933.90.08212933.805190.5
2.93-3.023.10.07710493.582172.7
3.02-3.1320.0746893.615147.6
3.13-3.251.60.0572093.348114.3
3.25-3.43.40.06411434.069178.1
3.4-3.574.20.05713123.973189.6
3.57-3.794.70.05514064.323196.2
3.79-4.084.40.05313224.078190.1
4.08-4.484.10.04712753.941184.5
4.48-5.114.40.04513483.759190.9
5.11-6.354.70.04614783.512198.1
6.35-154.60.04314813.408193.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.7 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å14.87 Å
Translation2.5 Å14.87 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: 2.4→14.87 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1269 5.01 %RANDOM
Rwork0.176 ---
obs0.1798 25339 86.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.308 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 82.07 Å2 / Biso mean: 23.2426 Å2 / Biso min: 6.88 Å2
Baniso -1Baniso -2Baniso -3
1--2.3489 Å2-0 Å20 Å2
2---3.0496 Å2-0 Å2
3---5.3984 Å2
Refinement stepCycle: LAST / Resolution: 2.4→14.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 19 451 5659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075316
X-RAY DIFFRACTIONf_angle_d1.0877188
X-RAY DIFFRACTIONf_chiral_restr0.073782
X-RAY DIFFRACTIONf_plane_restr0.004927
X-RAY DIFFRACTIONf_dihedral_angle_d14.111952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.49580.29031590.18212996315599
2.4958-2.60880.26111550.16533008316399
2.6088-2.74560.2751690.1633013318299
2.7456-2.91640.28911580.17792854301294
2.9164-3.13960.26821070.19461815192260
3.1396-3.4520.2746780.19091629170753
3.452-3.94330.23331570.18312931308895
3.9433-4.93780.21091290.15812712284186
4.9378-14.870.2391570.18173112326996

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