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- PDB-4fp3: Crystal structure of the NanB sialidase from streptococcus pneumo... -

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Basic information

Entry
Database: PDB / ID: 4fp3
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 2-[(Furan-2-ylmethyl)ammonio]sulfonate
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-[(furan-2-ylmethyl)amino]ethanesulfonic acid / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.743 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

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Assembly

Deposited unit
A: Sialidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9862
Polymers77,7811
Non-polymers2051
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.602, 82.674, 116.914
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-IJ2 / 2-[(furan-2-ylmethyl)amino]ethanesulfonic acid


Mass: 205.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
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: Feb 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→40 Å / Num. obs: 27781 / % possible obs: 89.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.135 / Χ2: 2.951 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.36-2.42.20.50513671.533189.6
2.4-2.442.70.45114031.673192.1
2.44-2.4930.45114271.711193.1
2.49-2.5430.41713981.665192.5
2.54-2.630.38614201.656192.3
2.6-2.6630.32914091.848192.2
2.66-2.7230.3114001.86191.9
2.72-2.83.10.27214081.86191.8
2.8-2.883.10.23913982.023191
2.88-2.973.20.21113932.071190.5
2.97-3.083.20.17913932.169190.9
3.08-3.23.30.15514012.492190.7
3.2-3.353.40.13713692.741189.7
3.35-3.523.40.12513913.173189.3
3.52-3.753.50.11413853.683188.7
3.75-4.033.60.10513773.908188
4.03-4.443.60.09713564.706187.3
4.44-5.083.70.09213714.996185.9
5.08-6.43.80.09513574.251184.8
6.4-403.70.08713585.68179.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.84 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.74 Å26.59 Å
Translation2.74 Å26.59 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: 2.743→26.593 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 950 4.96 %RANDOM
Rwork0.179 ---
obs0.1826 19151 95.66 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.094 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 100.58 Å2 / Biso mean: 29.217 Å2 / Biso min: 10.53 Å2
Baniso -1Baniso -2Baniso -3
1--5.6991 Å2-0 Å20 Å2
2---6.8888 Å2-0 Å2
3---12.5879 Å2
Refinement stepCycle: LAST / Resolution: 2.743→26.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 13 172 5374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085311
X-RAY DIFFRACTIONf_angle_d1.1227182
X-RAY DIFFRACTIONf_chiral_restr0.072781
X-RAY DIFFRACTIONf_plane_restr0.004927
X-RAY DIFFRACTIONf_dihedral_angle_d14.4711952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.743-2.88740.3431330.24252521265495
2.8874-3.0680.3061560.22692589274597
3.068-3.30450.2961290.20052600272997
3.3045-3.63630.28031350.18392629276497
3.6363-4.16070.23591350.16922591272696
4.1607-5.23550.18621240.13562593271794
5.2355-26.5930.21341380.16772678281693

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