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- PDB-4xjz: Crystal structure of apo NanB sialidase from streptococcus pneumo... -

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Basic information

Entry
Database: PDB / ID: 4xjz
TitleCrystal structure of apo NanB sialidase from streptococcus pneumoniae at pH 7.4 in PBS with DMSO
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
PHOSPHATE ION / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 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 / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_validate_close_contact / 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_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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)74,0057
Polymers73,5201
Non-polymers4866
Water11,512639
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint9 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.391, 82.656, 116.721
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 TIGR4 (bacteria)
Gene: nanB, SP_1687 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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.: 639 / 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: 50.92 %
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: ADSC QUANTUM 1 / Detector: CCD / 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→67.459 Å / Num. all: 110678 / Num. obs: 110678 / % possible obs: 99.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.05 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Rsym value: 0.091 / Net I/av σ(I): 6.35 / Net I/σ(I): 18.3 / Num. measured all: 722904
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.53-1.575.71.2142.84527679320.5861.2142.897.4
1.57-1.616.90.9840.65386678430.4150.9843.998.7
1.61-1.666.80.830.75233976760.3510.834.698.8
1.66-1.716.70.6680.84992174190.2860.6685.699.4
1.71-1.776.40.53714653372600.2390.5376.599.3
1.77-1.836.60.4061.44587869870.1790.4068.399.1
1.83-1.96.90.3011.94654367790.1280.3011199.6
1.9-1.986.70.2362.44416365510.1020.23613.799.5
1.98-2.076.60.1773.34132662940.0790.17716.599.6
2.07-2.176.20.14743704760090.070.14718.599.8
2.17-2.286.70.1254.53864057380.0550.12522.299.7
2.28-2.426.80.1045.83678654400.0460.10424.699.7
2.42-2.596.70.0896.93414751260.040.08927.499.9
2.59-2.86.10.0718.72940947930.0340.07129.999.8
2.8-3.066.80.05511.73026344350.0240.0553799.8
3.06-3.436.70.04115.62668440110.0190.04143.699.9
3.43-3.956.10.03319.62170835540.0160.03347.999.7
3.95-4.846.40.028221930030390.0130.02854.399.7
4.84-6.856.30.03201519623980.0140.0351.699.7
6.85-67.4595.70.02324.9787913940.0120.02351.899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.64 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å67.46 Å
Translation2.5 Å67.46 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VW0

2vw0


Resolution: 1.56→29.809 Å / FOM work R set: 0.8415 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 5199 5.01 %
Rwork0.1907 98673 -
obs0.1921 103872 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.59 Å2 / Biso mean: 24.12 Å2 / Biso min: 9.67 Å2
Refinement stepCycle: final / Resolution: 1.56→29.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 25 639 5849
Biso mean--26.32 31.69 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065340
X-RAY DIFFRACTIONf_angle_d1.0917223
X-RAY DIFFRACTIONf_chiral_restr0.078784
X-RAY DIFFRACTIONf_plane_restr0.004932
X-RAY DIFFRACTIONf_dihedral_angle_d13.5081957
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 (%)
1.56-1.57770.28121570.24483064322194
1.5777-1.59630.24581790.22873210338997
1.5963-1.61580.25441720.22813274344699
1.6158-1.63620.2331900.2223220341098
1.6362-1.65770.25851760.22193263343998
1.6577-1.68050.29771770.22483241341899
1.6805-1.70450.30031790.22383278345798
1.7045-1.72990.28211690.22483235340498
1.7299-1.75690.24241600.23083258341898
1.7569-1.78570.2521780.23763257343598
1.7857-1.81650.28971940.23473202339698
1.8165-1.84950.26111760.23033249342598
1.8495-1.88510.29731620.21813281344398
1.8851-1.92360.25561690.21883241341098
1.9236-1.96540.20761620.19563305346799
1.9654-2.01110.2151670.18323296346399
2.0111-2.06140.21421570.17663303346099
2.0614-2.11710.21631810.17853302348399
2.1171-2.17940.21851730.17763292346599
2.1794-2.24970.23291650.1693337350299
2.2497-2.33010.21981880.18153243343199
2.3301-2.42330.22631480.1833352350099
2.4233-2.53360.21431830.1853318350199
2.5336-2.66710.22031710.18933331350299
2.6671-2.83410.20751820.19143313349599
2.8341-3.05270.22051920.19023337352999
3.0527-3.35950.20351720.17883335350799
3.3595-3.84480.18211730.17213382355599
3.8448-4.84060.17751720.1643410358299
4.8406-29.81410.20641750.20623544371998

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