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

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Basic information

Entry
Database: PDB / ID: 4fov
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 3-Cyclohexyl-1-propylsulfonic acid
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
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 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)78,1584
Polymers77,7811
Non-polymers3783
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.269, 82.544, 116.803
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 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#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.: 503 / 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: 47.96 %
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: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.29→30 Å / Num. obs: 33189 / % possible obs: 97.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Χ2: 2.293 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.29-2.334.70.23916302.291199.4
2.33-2.374.80.22516402.236197.7
2.37-2.424.70.21716272.176198.8
2.42-2.474.80.19416702.2199.1
2.47-2.524.80.19616282.227198.2
2.52-2.584.80.17916592.235198.6
2.58-2.644.70.16616802.195199.7
2.64-2.714.80.15716422.207198.9
2.71-2.794.80.14316732.242199
2.79-2.884.80.12516472.305199
2.88-2.994.80.11416772.315199.1
2.99-3.114.80.09916632.384199
3.11-3.254.90.08316782.331198.8
3.25-3.424.90.07216812.435199.1
3.42-3.634.90.0616682.378198.4
3.63-3.914.90.05316642.324198.1
3.91-4.314.90.04816662.309197.3
4.31-4.934.90.04616702.421196.3
4.93-6.250.04816732.258195.2
6.2-304.90.04316532.372189.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.43 Å
Translation2.5 Å22.43 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: 2.29→22.433 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8297 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1639 4.95 %RANDOM
Rwork0.1797 ---
obs0.1824 33142 97.97 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.591 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 88.89 Å2 / Biso mean: 21.9204 Å2 / Biso min: 6.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.2857 Å2-0 Å20 Å2
2---5.2938 Å2-0 Å2
3---8.5795 Å2
Refinement stepCycle: LAST / Resolution: 2.29→22.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 22 503 5714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075342
X-RAY DIFFRACTIONf_angle_d1.0657230
X-RAY DIFFRACTIONf_chiral_restr0.073789
X-RAY DIFFRACTIONf_plane_restr0.004933
X-RAY DIFFRACTIONf_dihedral_angle_d14.11971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.35730.27061360.18332554269098
2.3573-2.43330.2821170.18582632274999
2.4333-2.52020.30411380.19192591272999
2.5202-2.62090.24621380.17852631276999
2.6209-2.740.24951500.17452624277499
2.74-2.88420.26391370.1832612274999
2.8842-3.06450.24781590.18622626278599
3.0645-3.30040.23471320.17412660279299
3.3004-3.63130.21441370.17362648278599
3.6313-4.15390.22921380.17942649278798
4.1539-5.22250.17841240.15732629275396
5.2225-22.4330.21441330.20732647278093

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