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- PDB-6s0f: Crystal structure of an inverting family GH156 exosialidase from ... -

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Basic information

Entry
Database: PDB / ID: 6s0f
TitleCrystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid
Componentsexosialidase from uncultured bacterium pG7
KeywordsHYDROLASE / (beta/alpha )8 barrel / sialidase / inverting / homodimer
Function / homologyACETATE ION / deamino-beta-neuraminic acid / THIOCYANATE ION
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 14, 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

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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)119,50421
Polymers117,5732
Non-polymers1,93119
Water8,773487
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 area7650 Å2
ΔGint-18 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.661, 78.924, 112.992
Angle α, β, γ (deg.)90.000, 94.890, 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-KDN / deamino-beta-neuraminic acid / beta-deaminoneuraminic acid / 3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid / sialic acid / Sialic acid


Type: D-saccharide, beta linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16O9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DKdnpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
2-keto-3-deoxy-b-D-nonulopyranosic acidCOMMON NAMEGMML 1.0
b-D-KdnpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdnSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 504 molecules

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


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15 M potassium thiocyanite, 20% PEG 1500, 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: 2→112.58 Å / Num. obs: 75378 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.956 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.093 / Rrim(I) all: 0.188 / Net I/σ(I): 5.4 / Num. measured all: 301514 / Scaling rejects: 2147
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
2-2.044.20.5761842444200.8480.3180.662.4100
10-112.584.30.09527966530.9860.050.1089.799.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZD

6rzd


Resolution: 2→112.58 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.883 / SU B: 13.77 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 3867 5.1 %RANDOM
Rwork0.2169 ---
obs0.2194 71456 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.01 Å2 / Biso mean: 21.551 Å2 / Biso min: 7.61 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å20 Å20.45 Å2
2---1.97 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: final / Resolution: 2→112.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8027 0 125 487 8639
Biso mean--31.64 27.37 -
Num. residues----993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177707
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.65611419
X-RAY DIFFRACTIONr_angle_other_deg1.3281.57617743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.81251000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.33419.526527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.715151313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.08815105
X-RAY DIFFRACTIONr_chiral_restr0.0880.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022038
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 308 -
Rwork0.272 5253 -
all-5561 -
obs--99.8 %
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)
10.35640.1390.20770.74820.30491.64430.02040.0168-0.04350.0458-0.00770.03420.10010.0454-0.01280.03230.0050.00340.0058-0.00050.011211.8875-25.345247.2169
20.3731-0.2128-0.35120.71550.22231.57970.0285-0.00560.0575-0.0482-0.00480.0049-0.14350.0489-0.02370.0309-0.01080.00070.01330.00430.014915.1697-7.348511.8986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 1601
2X-RAY DIFFRACTION2B6 - 1501

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