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

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Basic information

Entry
Database: PDB / ID: 4xjw
TitleCrystal structure of the NanB sialidase from streptococcus pneumoniae in complex with Optactin at pH 7.4 in PBS with DMSO as the cryoprotectant
ComponentsSialidase B
KeywordsHYDROLASE / intramolecular trans-sialidase / glycosidase / drug design / neuraminidase / allosteric inhibitor / serendipitous allosteric sites / crystallization artefacts
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-OPX / PHOSPHATE ION / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 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
DepositionJan 9, 2015Deposition 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

Downloads & links

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Assembly

Deposited unit
A: Sialidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2217
Polymers73,5201
Non-polymers7016
Water12,412689
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint8 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.950, 82.850, 116.580
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 serotype 4 (strain ATCC BAA-334 / 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.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 50.69 %
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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.53→55.99 Å / Num. obs: 156017 / % possible obs: 98 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.7
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.58 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å50.47 Å
Translation2.5 Å50.47 Å

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Processing

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

2vw0


Resolution: 1.53→47.673 Å / FOM work R set: 0.8671 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 5473 4.99 %
Rwork0.1903 104284 -
obs0.1914 109757 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.26 Å2 / Biso mean: 19.52 Å2 / Biso min: 5.8 Å2
Refinement stepCycle: final / Resolution: 1.53→47.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 40 689 5914
Biso mean--18.6 27.17 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065356
X-RAY DIFFRACTIONf_angle_d1.097250
X-RAY DIFFRACTIONf_chiral_restr0.076787
X-RAY DIFFRACTIONf_plane_restr0.004932
X-RAY DIFFRACTIONf_dihedral_angle_d15.1841978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5262-1.54350.27271640.24423541370599
1.5435-1.56170.27371780.241434983676100
1.5617-1.58070.26861960.219334963692100
1.5807-1.60070.22772050.213734873692100
1.6007-1.62180.25971830.208535033686100
1.6218-1.6440.26611880.202635063694100
1.644-1.66750.20731840.19535143698100
1.6675-1.69240.21511880.191235163704100
1.6924-1.71880.23731870.194535103697100
1.7188-1.7470.21991860.194434933679100
1.747-1.77710.24161950.192435073702100
1.7771-1.80950.23731920.193635583750100
1.8095-1.84430.20951990.175435063705100
1.8443-1.88190.20041750.180235463721100
1.8819-1.92280.42481480.37352796294480
1.9228-1.96760.30711530.23653074322787
1.9676-2.01680.18821740.178235463720100
2.0168-2.07130.20431900.169335303720100
2.0713-2.13220.19511870.173935523739100
2.1322-2.20110.20681690.1735473716100
2.2011-2.27970.36381430.28942599274273
2.2797-2.3710.18141870.175535353722100
2.371-2.47890.22571740.17935683742100
2.4789-2.60960.21381820.179436043786100
2.6096-2.77310.21981990.184335323731100
2.7731-2.98720.191980.184935883786100
2.9872-3.28770.16411920.172135763768100
3.2877-3.76330.19411860.17133599378599
3.7633-4.74060.14911720.160536553827100
4.7406-47.69640.17951990.191138024001100

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