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- PDB-6s04: Crystal structure of an inverting family GH156 exosialidase from ... -

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Basic information

Entry
Database: PDB / ID: 6s04
TitleCrystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-glycolylneuraminic acid
Componentsexosialidase from uncultured bacterium pG7
KeywordsHYDROLASE / (beta/alpha )8 barrel / sialidase / inverting / homodimer
Function / homologyACETATE ION / N-glycolyl-beta-neuraminic acid
Function and homology information
Biological speciesuncultured bacterium pG7 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine.pdbx_diffrn_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)119,95412
Polymers118,6992
Non-polymers1,25510
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-Malls confirmed the dimeric assembly in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-17 kcal/mol
Surface area35040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.053, 79.548, 113.520
Angle α, β, γ (deg.)90.000, 94.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein exosialidase from uncultured bacterium pG7


Mass: 59349.383 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
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-NGE / N-glycolyl-beta-neuraminic acid / N-glycolylneuraminic acid / sialic acid


Type: D-saccharide, beta linking / Mass: 325.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19NO10 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5GcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-glycolyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5GcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5GcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 50.58 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.8 M sodium formate, 12% 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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→65.07 Å / Num. obs: 78077 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.963 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.126 / Rrim(I) all: 0.269 / Net I/σ(I): 3.7 / Num. measured all: 323640 / Scaling rejects: 570
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
2-2.044.20.6351873644740.7390.3420.7232.1100
10.2-65.073.60.12522876330.8870.0770.1484.799.1

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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: 2→64.89 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.863 / SU B: 11.843 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / 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
Rfree0.2763 3941 5 %RANDOM
Rwork0.2294 ---
obs0.2317 74113 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.46 Å2 / Biso mean: 17.122 Å2 / Biso min: 1.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-0.45 Å2
2---0.14 Å20 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 2→64.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8023 0 84 550 8657
Biso mean--21.83 20.12 -
Num. residues----992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177643
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.66311356
X-RAY DIFFRACTIONr_angle_other_deg1.2781.57617591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7025993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57819.542524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.666151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.16215104
X-RAY DIFFRACTIONr_chiral_restr0.0850.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022034
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 323 -
Rwork0.278 5396 -
all-5719 -
obs--99.88 %
Refinement TLS params.

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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2520.129-0.22780.6427-0.0291.51640.05160.01110.07430.068-0.05270.0253-0.1175-0.15190.00110.01870.0060.01150.0199-0.00270.029411.853126.120144.7868
20.2127-0.1670.13610.6799-0.12021.47590.04710.0031-0.0356-0.096-0.03680.00960.0982-0.1209-0.01040.0232-0.0009-0.01140.0133-0.00180.018315.35618.04529.1434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 1001
2X-RAY DIFFRACTION2B6 - 1201

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