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- PDB-4xe9: Crystal structure of the NanB sialidase from Streptococcus pneumo... -

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Basic information

Entry
Database: PDB / ID: 4xe9
TitleCrystal structure of the NanB sialidase from Streptococcus pneumoniae in complex with Optactin
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
Chem-OPX / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsBrear, P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
SULSA 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
DepositionDec 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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

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Assembly

Deposited unit
A: Sialidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2047
Polymers73,5201
Non-polymers6846
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint13 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.201, 82.702, 116.423
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 / Mutation: D643G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: nanB, SP_1687 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical ChemComp-OPX / (1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid


Mass: 293.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H23NO5S
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
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: 1.84→30 Å / Num. obs: 61144 / % possible obs: 94.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 18.28 Å2 / Rmerge(I) obs: 0.058 / Χ2: 3.26 / Net I/av σ(I): 43.229 / Net I/σ(I): 23.9 / Num. measured all: 273389
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.84-1.873.60.16127982.33688.6
1.87-1.914.40.15530242.40394.4
1.91-1.944.50.13230442.48695.9
1.94-1.984.60.12130482.82695.9
1.98-2.034.60.11130652.96695.8
2.03-2.074.60.10430643.17996.2
2.07-2.124.60.09730863.30996.3
2.12-2.184.60.09230923.44496.8
2.18-2.254.60.08731223.63496.8
2.25-2.324.70.08330773.59296.9
2.32-2.44.70.07731443.60197.8
2.4-2.54.70.07131303.58997.6
2.5-2.614.70.06831583.52997.6
2.61-2.754.70.06331593.60297.7
2.75-2.924.60.05931303.52997.6
2.92-3.154.40.05230903.36695.1
3.15-3.464.10.04728533.35787.5
3.46-3.9640.04227973.18285.2
3.96-4.994.20.04129393.40788.8
4.99-304.30.0433243.3795.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.74 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.83 Å
Translation2.5 Å25.83 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: 1.84→25.83 Å / FOM work R set: 0.8739 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 2993 4.9 %
Rwork0.1724 58096 -
obs0.1742 61089 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.03 Å2 / Biso mean: 22.4 Å2 / Biso min: 8.58 Å2
Refinement stepCycle: final / Resolution: 1.84→25.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 39 698 5922
Biso mean--24.21 29.35 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065382
X-RAY DIFFRACTIONf_angle_d1.0987291
X-RAY DIFFRACTIONf_chiral_restr0.079794
X-RAY DIFFRACTIONf_plane_restr0.004939
X-RAY DIFFRACTIONf_dihedral_angle_d13.4821980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.86960.2231270.16732517X-RAY DIFFRACTION88
1.8696-1.90190.19791390.17252756X-RAY DIFFRACTION94
1.9019-1.93640.2481380.16532739X-RAY DIFFRACTION96
1.9364-1.97370.22841420.16772786X-RAY DIFFRACTION96
1.9737-2.01390.24331380.1762755X-RAY DIFFRACTION96
2.0139-2.05770.21241300.16772786X-RAY DIFFRACTION96
2.0577-2.10560.22551620.16882790X-RAY DIFFRACTION97
2.1056-2.15820.21151390.16542781X-RAY DIFFRACTION96
2.1582-2.21650.20431330.16372812X-RAY DIFFRACTION97
2.2165-2.28170.21081620.16152795X-RAY DIFFRACTION97
2.2817-2.35530.21131480.17252813X-RAY DIFFRACTION97
2.3553-2.43940.22411360.17112860X-RAY DIFFRACTION98
2.4394-2.5370.24811480.17542828X-RAY DIFFRACTION97
2.537-2.65240.18161530.16882850X-RAY DIFFRACTION98
2.6524-2.79210.20381500.17142869X-RAY DIFFRACTION98
2.7921-2.96670.20721670.17472816X-RAY DIFFRACTION97
2.9667-3.19540.19971400.1722764X-RAY DIFFRACTION94
3.1954-3.51630.22271290.17472559X-RAY DIFFRACTION86
3.5163-4.02350.19651310.17472533X-RAY DIFFRACTION85
4.0235-5.06290.17031310.16132689X-RAY DIFFRACTION89
5.0629-25.83220.20731500.19722998X-RAY DIFFRACTION96

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