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

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Basic information

Entry
Database: PDB / ID: 4xhb
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with pentanediol and CHES
ComponentsSialidase B
KeywordsHYDROLASE / intramolecular trans-sialidase / glycosidase / drug design / neuraminidase / allosteric inhibitor / serendipitous allosteric sites / crystallization artefacts
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
(1R,2S)-cyclopentane-1,2-diol / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsBrear, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: To be published
Title: The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB
Authors: Rogers, G.W. / Brear, P. / Yang, L. / Chen, A.S. / Mitchell, J.B.O. / Taylor, G.L. / Westwood, N.J.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)73,8293
Polymers73,5201
Non-polymers3092
Water12,160675
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint10 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.494, 82.585, 117.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Sialidase B / Neuraminidase B


Mass: 73519.852 Da / Num. of mol.: 1 / Fragment: UNP residues 39-696 / Mutation: D643G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: nanB, SP_1687 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical ChemComp-17Y / (1R,2S)-cyclopentane-1,2-diol


Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 7% PEG 8000, 0.1M IMIDAZOLE

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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 / Detector: CCD / Date: Jun 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→10 Å / Num. obs: 55181 / % possible obs: 91 % / Redundancy: 4.9 % / Biso Wilson estimate: 17.81 Å2 / Rmerge(I) obs: 0.055 / Χ2: 2.143 / Net I/av σ(I): 38.489 / Net I/σ(I): 18.7 / Num. measured all: 271960
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.88-1.914.40.18828281.8693.5
1.91-1.954.40.16727721.94794.1
1.95-1.984.40.14528171.93693.7
1.98-2.024.50.13328021.93793.5
2.02-2.074.50.12128101.99493.6
2.07-2.124.60.10928232.04193.8
2.12-2.174.60.09927982.02793.1
2.17-2.234.70.09128112.05993.7
2.23-2.294.80.08527952.10193.1
2.29-2.364.90.0827962.01693
2.36-2.4550.07627892.10492.4
2.45-2.545.10.07227782.0791.7
2.54-2.665.10.06627732.05391.8
2.66-2.795.20.06227682.08591.1
2.79-2.965.20.05527422.09590
2.96-3.195.30.04927112.12188.6
3.19-3.495.30.04526422.27286.7
3.49-3.975.50.03926902.35587.5
3.97-4.95.60.03926473.01484.7
4.9-105.80.0425892.47280.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 29.58 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.81 Å
Translation2.5 Å22.81 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VW0

2vw0


Resolution: 1.88→9.981 Å / FOM work R set: 0.8913 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 2699 4.89 %
Rwork0.1497 52450 -
obs0.1516 55149 91.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.77 Å2 / Biso mean: 20 Å2 / Biso min: 5.68 Å2
Refinement stepCycle: final / Resolution: 1.88→9.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 20 675 5880
Biso mean--18.56 27.6 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075347
X-RAY DIFFRACTIONf_angle_d1.0967239
X-RAY DIFFRACTIONf_chiral_restr0.079790
X-RAY DIFFRACTIONf_plane_restr0.004932
X-RAY DIFFRACTIONf_dihedral_angle_d13.1621973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.9140.21381360.15932819295594
1.914-1.95050.21851460.14322799294594
1.9505-1.990.1961540.14612787294194
1.99-2.03290.20941220.14512847296994
2.0329-2.07980.20161530.14782811296494
2.0798-2.13130.19321490.14622794294393
2.1313-2.18840.22031420.15262808295093
2.1884-2.25210.24921350.15322826296193
2.2521-2.32390.18861640.15362761292593
2.3239-2.40580.22491290.15832810293993
2.4058-2.50070.22781510.15942806295792
2.5007-2.61250.19341350.16342773290892
2.6125-2.74760.20821510.1592765291691
2.7476-2.91570.17981530.15882732288591
2.9157-3.13430.18131500.15422709285989
3.1343-3.4380.17051290.14322672280187
3.438-3.9090.15651340.13722671280587
3.909-4.83020.15291310.13272668279985
4.8302-9.98070.1691350.1612592272781

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