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- PDB-4xyx: NanB plus Optactamide -

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Basic information

Entry
Database: PDB / ID: 4xyx
TitleNanB plus Optactamide
ComponentsSialidase B
KeywordsHYDROLASE / Inhibitor binding
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
Optactamide / PHOSPHATE ION / Sialidase B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRogers, G.W. / Brear, P. / Yang, L. / Taylor, G.L. / Westwood, N.J.
CitationJournal: To Be Published
Title: The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB
Authors: Brear, P. / Rogers, G.W. / Yang, L. / Chen, A.S. / Mitchell, J.B.O. / Taylor, G.L. / Westwood, N.J.
History
DepositionFeb 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 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)75,77520
Polymers73,7781
Non-polymers1,99719
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-110 kcal/mol
Surface area25240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.603, 82.648, 116.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sialidase B / Neuraminidase B


Mass: 73778.141 Da / Num. of mol.: 1 / Fragment: UNP residues 40-697
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: nanB, SP_1687 / Production host: Escherichia coli (E. coli) / References: UniProt: Q54727, exo-alpha-sialidase
#2: Chemical ChemComp-43Z / Optactamide


Mass: 287.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15ClFNO3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100mM Imidazole pH8, 5% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 42642 / % possible obs: 98.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.071 / Χ2: 2.902 / Net I/av σ(I): 38.04 / Net I/σ(I): 18.4 / Num. measured all: 234475
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.144.20.22119532.43392.6
2.14-2.185.10.20820612.28496.4
2.18-2.225.40.19820822.48898.3
2.22-2.265.40.18620892.41998.7
2.26-2.315.50.17221052.28898.1
2.31-2.375.50.15621032.36698.4
2.37-2.425.50.14621402.37699.4
2.42-2.495.60.14221052.40298.8
2.49-2.565.50.13120942.42698.6
2.56-2.655.50.11921282.43399.2
2.65-2.745.60.10821532.48899.4
2.74-2.855.60.09321262.54299.3
2.85-2.985.60.08421492.62699.3
2.98-3.145.60.07321382.8399.3
3.14-3.335.70.06221362.98999.4
3.33-3.595.80.05421953.14399.9
3.59-3.955.90.04921793.5599.8
3.95-4.525.70.04821854.15599.5
4.52-5.75.70.04922184.01599.7
5.7-505.50.05623035.08597.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation22.4 Å2.35 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VW2

2vw2


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.2161 / WRfactor Rwork: 0.1706 / FOM work R set: 0.8358 / SU B: 4.201 / SU ML: 0.115 / SU R Cruickshank DPI: 0.2233 / SU Rfree: 0.1869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 2099 4.9 %RANDOM
Rwork0.1861 40351 --
obs0.1885 40351 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.36 Å2 / Biso mean: 24.982 Å2 / Biso min: 10.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---0.54 Å2-0 Å2
3---1.79 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 109 284 5596
Biso mean--52.22 27.4 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025411
X-RAY DIFFRACTIONr_angle_refined_deg2.3711.9697329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5815661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11725.02249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83115928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3871521
X-RAY DIFFRACTIONr_chiral_restr0.1460.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214050
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 148 -
Rwork0.176 2594 -
all-2742 -
obs--91.52 %

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