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- PDB-6s0e: Crystal structure of an inverting family GH156 exosialidase from ... -

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Basic information

Entry
Database: PDB / ID: 6s0e
TitleCrystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-Acetyl-2,3-dehydro-2-deoxyneuraminic acid
Componentsexosialidase from uncultured bacterium pG7
KeywordsHYDROLASE / (beta/alpha )8 barrel / sialidase / inverting / homodimer
Function / homologyACETATE ION / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
Function and homology information
Biological speciesuncultured bacterium pG7 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBule, P. / Blagova, E. / Chuzel, L. / Taron, C.H. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action.
Authors: Bule, P. / Chuzel, L. / Blagova, E. / Wu, L. / Gray, M.A. / Henrissat, B. / Rapp, E. / Bertozzi, C.R. / Taron, C.H. / Davies, G.J.
History
DepositionJun 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: chem_comp / refine ...chem_comp / refine / struct_site / struct_site_gen
Item: _chem_comp.type / _refine.pdbx_diffrn_id / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: exosialidase from uncultured bacterium pG7
B: exosialidase from uncultured bacterium pG7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,53419
Polymers117,5732
Non-polymers1,96117
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS confirmed the dimer assembly in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-8 kcal/mol
Surface area33330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.418, 78.756, 112.820
Angle α, β, γ (deg.)90.000, 94.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein exosialidase from uncultured bacterium pG7


Mass: 58786.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium pG7 (environmental samples)
Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: exo-alpha-sialidase
#5: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO8 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 505 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M potassium bromide, 15% PEG 4000, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.9→78.76 Å / Num. obs: 87227 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.91 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.099 / Rrim(I) all: 0.198 / Net I/σ(I): 5 / Num. measured all: 345513 / Scaling rejects: 2353
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.933.80.5531696844520.7560.3420.6552.599.9
10.23-78.764.20.11525506030.9850.0610.1317.599.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZD

6rzd


Resolution: 1.9→64.58 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.845 / SU B: 13.302 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3067 4328 5 %RANDOM
Rwork0.2504 ---
obs0.2531 82866 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.69 Å2 / Biso mean: 20.945 Å2 / Biso min: 0.51 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å20.04 Å2
2---1.05 Å20 Å2
3----1.62 Å2
Refinement stepCycle: final / Resolution: 1.9→64.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 128 490 8638
Biso mean--26.63 22.93 -
Num. residues----992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138381
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177698
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.65711382
X-RAY DIFFRACTIONr_angle_other_deg1.3191.57717711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6265992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06319.486525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4151305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.73315105
X-RAY DIFFRACTIONr_chiral_restr0.0830.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022041
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 315 -
Rwork0.406 6091 -
all-6406 -
obs--99.6 %
Refinement TLS params.

T23: -0.0024 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2320.10670.0970.90420.02091.84260.03730.009-0.0340.0697-0.0318-0.01160.20550.1566-0.00550.07370.0203-0.01910.03120.0111.7798-25.145847.3306
20.2711-0.0815-0.37320.77480.0542.08770.0481-0.04420.0489-0.1349-0.0307-0.0241-0.13410.2035-0.01750.0769-0.01130.01030.03270.010715.1587-7.490511.8072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 1501
2X-RAY DIFFRACTION2B6 - 1601

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