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

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Basic information

Entry
Database: PDB / ID: 4fpo
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 2-[(3-chloro-4-methoxybenzyl)ammonio]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
Chem-LL9 / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.591 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
B: Sialidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2174
Polymers77,7811
Non-polymers4363
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.457, 82.487, 116.807
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-LL9 / 2-[(3-chloro-4-methoxybenzyl)amino]ethanesulfonic acid


Mass: 279.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14ClNO4S
#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.: 247 / 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: 48.05 %
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: Aug 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.591→30 Å / Num. obs: 23200 / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.127 / Χ2: 4.285 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.591-2.84.60.2939662.329199.8
2.8-2.854.60.279942.2951100
2.85-2.94.70.2449482.281100
2.9-2.964.60.2289972.4381100
2.96-3.034.60.2149532.752199.9
3.03-3.14.70.1999852.854199.7
3.1-3.174.70.1789873.117199.9
3.17-3.264.70.1659823.169199.7
3.26-3.364.70.1519763.795199.9
3.36-3.464.70.1469954.369199.9
3.46-3.594.70.1329784.53199.7
3.59-3.734.70.1269815.084199.9
3.73-3.94.70.12210025.531199.9
3.9-4.114.70.1149956.073199.8
4.11-4.364.70.10510026.239199.2
4.36-4.74.70.19997.17199.6
4.7-5.174.70.09510086.3221100
5.17-5.914.70.10210195.2191100
5.91-7.434.60.09910334.791100
7.43-304.30.07310834.898197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.591→24.9 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.43 / σ(F): 1.33 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 1157 4.99 %RANDOM
Rwork0.2011 ---
obs0.2045 23200 98.43 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.904 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 121.42 Å2 / Biso mean: 26.9098 Å2 / Biso min: 8.09 Å2
Baniso -1Baniso -2Baniso -3
1--3.6336 Å2-0 Å20 Å2
2---2.9426 Å2-0 Å2
3---6.5761 Å2
Refinement stepCycle: LAST / Resolution: 2.591→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 25 247 5461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085327
X-RAY DIFFRACTIONf_angle_d1.1267204
X-RAY DIFFRACTIONf_chiral_restr0.075784
X-RAY DIFFRACTIONf_plane_restr0.003929
X-RAY DIFFRACTIONf_dihedral_angle_d14.2231958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.591-2.7090.38681520.2722680283298
2.709-2.85160.31631370.24652757289499
2.8516-3.030.32751630.23072680284399
3.03-3.26350.29621470.201327552902100
3.2635-3.5910.25761430.19127872930100
3.591-4.10860.25131460.204228032949100
4.1086-5.16880.21091270.15682796292398
5.1688-24.9010.2361420.19732785292794

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