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- PDB-4xma: Crystal structure of the K499G mutant of NanB sialidase from stre... -

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Basic information

Entry
Database: PDB / ID: 4xma
TitleCrystal structure of the K499G mutant of 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 serotype 4 TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 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 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support / 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 / _struct_site_gen.auth_seq_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)73,9755
Polymers73,4481
Non-polymers5284
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint11 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.468, 82.672, 116.553
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: 73447.719 Da / Num. of mol.: 1 / Fragment: UNP residues 39-696 / Mutation: K499G D643G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 TIGR4 (bacteria)
Gene: nanB, SP_1687 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
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: Aug 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→30 Å / Num. obs: 43942 / % possible obs: 98.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.73 Å2 / Rmerge(I) obs: 0.096 / Χ2: 3.774 / Net I/av σ(I): 24.438 / Net I/σ(I): 14.4 / Num. measured all: 181755
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.09-2.133.70.28821472.37696.7
2.13-2.163.70.27421162.36997.6
2.16-2.213.70.24521352.32797.5
2.21-2.253.70.23121622.39297.2
2.25-2.33.60.22421412.44698.7
2.3-2.353.70.20321682.44899
2.35-2.413.70.221702.50799.4
2.41-2.483.70.18721822.73799.3
2.48-2.553.80.18222162.63999.7
2.55-2.633.90.16322002.81699.8
2.63-2.7340.1522012.83399.9
2.73-2.844.20.1422113.23199.9
2.84-2.974.30.12122243.64899.9
2.97-3.124.50.10222033.81899.6
3.12-3.324.60.08822353.97699.6
3.32-3.574.70.07722044.46299.5
3.57-3.934.80.0722405.23399.5
3.93-4.54.80.06922466.40198.7
4.5-5.664.70.07122417.01498.3
5.66-304.60.0723005.77395

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.14 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.29 Å
Translation2.5 Å25.29 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 / Resolution: 2.09→25.288 Å / FOM work R set: 0.8297 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 2215 5.06 %
Rwork0.1813 41595 -
obs0.1843 43810 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.81 Å2 / Biso mean: 16.55 Å2 / Biso min: 2.32 Å2
Refinement stepCycle: final / Resolution: 2.09→25.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5180 0 31 482 5693
Biso mean--16.65 21.14 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075350
X-RAY DIFFRACTIONf_angle_d1.0687245
X-RAY DIFFRACTIONf_chiral_restr0.075786
X-RAY DIFFRACTIONf_plane_restr0.004935
X-RAY DIFFRACTIONf_dihedral_angle_d15.2971978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0897-2.13510.24911460.16842493263996
2.1351-2.18470.26811270.17732552267997
2.1847-2.23940.241180.17682535265397
2.2394-2.29990.25321320.17952577270998
2.2999-2.36750.26121170.18832570268799
2.3675-2.44380.27691360.19212608274499
2.4438-2.53110.29021570.20142573273099
2.5311-2.63240.24991520.19952586273899
2.6324-2.7520.28421280.20352621274999
2.752-2.89690.27891320.20626122744100
2.8969-3.07810.25921410.19862613275499
3.0781-3.31530.25461400.19492640278099
3.3153-3.64810.22981410.171726242765100
3.6481-4.17390.22581270.16022659278699
4.1739-5.25090.19791680.15942617278598
5.2509-25.28980.2071530.18262715286896

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