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

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Basic information

Entry
Database: PDB / ID: 4foy
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 2-(Benzylammonio)ethanesulfonate
ComponentsSialidase B
KeywordsHYDROLASE/INHIBITOR / hydrolase / intramolecular trans-sialidase / glycosidase / drug design / neuraminidase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / carbohydrate metabolic process
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-(benzylamino)ethanesulfonic acid / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.843 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 21, 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)78,2315
Polymers77,7811
Non-polymers4504
Water15,277848
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.318, 82.596, 117.019
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-D53 / 2-(benzylamino)ethanesulfonic acid


Mass: 215.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO3S
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 48.12 %
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: May 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 64163 / % possible obs: 98.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.067 / Χ2: 2.363 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.84-1.873.30.27628302.154189.2
1.87-1.914.20.27432232.152199.8
1.91-1.944.40.23731712.3261100
1.94-1.984.50.232212.337199.7
1.98-2.034.60.1731892.344199.7
2.03-2.074.60.14931982.394199.7
2.07-2.124.60.14232062.351199.6
2.12-2.184.60.12632042.388199.6
2.18-2.254.70.11831972.411199.5
2.25-2.324.70.1131952.357199.4
2.32-2.44.70.10631802.409199.4
2.4-2.54.80.09632552.395199.5
2.5-2.614.80.0931882.358199.3
2.61-2.754.80.08132372.361199.3
2.75-2.924.80.0732082.349199.3
2.92-3.154.80.05932362.361199.6
3.15-3.464.80.04932852.453199.8
3.46-3.964.70.04232792.498199.5
3.96-4.994.70.03632962.19199.1
4.99-304.70.03833652.544196.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.82 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å20.63 Å
Translation2.5 Å20.63 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: 1.843→20.633 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.2 / σ(F): 1.33 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 3145 4.91 %RANDOM
Rwork0.176 ---
obs0.1779 64034 99.33 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.056 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 91.43 Å2 / Biso mean: 20.4089 Å2 / Biso min: 5.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.2652 Å2-0 Å20 Å2
2---3.4224 Å2-0 Å2
3---3.6876 Å2
Refinement stepCycle: LAST / Resolution: 1.843→20.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 26 848 6063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075376
X-RAY DIFFRACTIONf_angle_d1.1137280
X-RAY DIFFRACTIONf_chiral_restr0.083796
X-RAY DIFFRACTIONf_plane_restr0.004939
X-RAY DIFFRACTIONf_dihedral_angle_d13.5441992
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.843-1.87190.31871390.25412714285399
1.8719-1.90250.27911310.231327592890100
1.9025-1.93530.30271500.199127512901100
1.9353-1.97050.24671290.173327602889100
1.9705-2.00840.19951470.1727432890100
2.0084-2.04930.19891260.167427622888100
2.0493-2.09380.22131600.163527262886100
2.0938-2.14250.19991350.16427462881100
2.1425-2.1960.23671380.162827632901100
2.196-2.25530.23291390.16562759289899
2.2553-2.32160.231590.17452712287199
2.3216-2.39640.22691270.17882770289799
2.3964-2.48190.2411450.17192749289499
2.4819-2.58110.19951410.17592761290299
2.5811-2.69840.21071540.17992750290499
2.6984-2.84030.22121410.18952759290099
2.8403-3.01770.22251640.18652728289299
3.0177-3.24990.21121490.1712801295099
3.2499-3.57540.18971450.157928102955100
3.5754-4.08930.17371470.16342810295799
4.0893-5.13890.17711340.15962842297699
5.1389-20.6330.22671450.20952914305997

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