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

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Basic information

Entry
Database: PDB / ID: 4fpj
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 2-[(3-Methoxybenzyl)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-methoxybenzyl)amino]ethanesulfonic acid / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.981 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

Downloads & links

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Assembly

Deposited unit
A: Sialidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1824
Polymers77,7811
Non-polymers4023
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.345, 82.577, 116.386
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-D8I / 2-[(3-methoxybenzyl)amino]ethanesulfonic acid


Mass: 245.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO4S
#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.: 534 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
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: Oct 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. obs: 51314 / % possible obs: 98.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.096 / Χ2: 5.941 / Net I/σ(I): 18.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.98-2.013.50.28425513.437199.3
2.01-2.054.30.25725213.5831100
2.05-2.094.30.2425693.831100
2.09-2.134.30.22425593.834199.7
2.13-2.184.30.20225574.074199.8
2.18-2.234.30.19125574.28199.7
2.23-2.294.30.18825474.615199.6
2.29-2.354.20.17125594.501199.5
2.35-2.424.20.16825384.81199.6
2.42-2.494.20.15125784.925199.5
2.49-2.584.20.14825365.221198.6
2.58-2.694.20.13325425.646199.1
2.69-2.814.20.12425716.104198.5
2.81-2.964.20.11225676.746198.8
2.96-3.144.20.125437.785198.8
3.14-3.384.40.0925978.418199.5
3.38-3.724.30.0826079.235199.4
3.72-4.2640.0725099.112195
4.26-5.364.30.0726249.992198.1
5.36-304.40.06326827.946195.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.04 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å20.61 Å
Translation2.5 Å20.61 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: 1.981→20.606 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.22 / σ(F): 1.33 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 2511 4.92 %RANDOM
Rwork0.198 ---
obs0.2001 50993 98.45 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.688 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 90.48 Å2 / Biso mean: 28.6199 Å2 / Biso min: 12.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.2506 Å2-0 Å20 Å2
2---5.629 Å2-0 Å2
3---7.8796 Å2
Refinement stepCycle: LAST / Resolution: 1.981→20.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 24 534 5747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075359
X-RAY DIFFRACTIONf_angle_d1.1047257
X-RAY DIFFRACTIONf_chiral_restr0.08791
X-RAY DIFFRACTIONf_plane_restr0.004938
X-RAY DIFFRACTIONf_dihedral_angle_d13.7271981
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 (%)
1.981-2.01920.24221180.21022711282999
2.0192-2.06040.24721420.194126752817100
2.0604-2.10510.26841530.192626852838100
2.1051-2.15410.2441410.192626752816100
2.1541-2.20790.27561260.19342692281899
2.2079-2.26750.29121400.20012661280199
2.2675-2.33410.30111590.21762649280898
2.3341-2.40940.24021150.22472697281299
2.4094-2.49530.32611440.21872681282598
2.4953-2.59510.25261410.2282654279598
2.5951-2.71290.28511520.2182629278198
2.7129-2.85560.2791300.21952673280398
2.8556-3.0340.25771610.21342664282598
3.034-3.26740.2521470.19182708285599
3.2674-3.59460.22071420.18727552897100
3.5946-4.11120.20631330.1862654278796
4.1112-5.16620.17081270.16152765289298
5.1662-20.6060.22261400.21422854299497

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