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

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Basic information

Entry
Database: PDB / ID: 6rzd
TitleCrystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7
Componentsexosialidase from uncultured bacterium pG7
KeywordsHYDROLASE / (beta/alpha )8 barrel / sialidase / inverting / homodimer
Function / homologyACETATE 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 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 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 / refine / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.d_res_low

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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)119,20921
Polymers117,5732
Non-polymers1,63619
Water7,566420
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 area8130 Å2
ΔGint-65 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.112, 79.273, 112.214
Angle α, β, γ (deg.)90.000, 94.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 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

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Non-polymers , 5 types, 439 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.11 % / Mosaicity: 0 °
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.8 M sodium formate, 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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→64.67 Å / Num. obs: 75801 / % possible obs: 100 % / Redundancy: 5.4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.094 / Rrim(I) all: 0.219 / Net I/σ(I): 5.8 / Num. measured all: 412825 / Scaling rejects: 1502
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
2-2.045.60.8092479944470.5930.3770.8941.899.7
10-64.675.10.08433346510.9930.0390.09314.199.6

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Processing

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

Resolution: 2→64.67 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.883 / SU B: 13.536 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.201
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 3839 5.1 %RANDOM
Rwork0.2337 ---
obs0.2363 71915 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.04 Å2 / Biso mean: 23.225 Å2 / Biso min: 7.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å2-0.89 Å2
2---0.09 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 2→64.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 106 420 8546
Biso mean--35.89 24.02 -
Num. residues----992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138405
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177731
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.65211417
X-RAY DIFFRACTIONr_angle_other_deg1.3121.57217783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75651002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.41719.49529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.723151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.07815106
X-RAY DIFFRACTIONr_chiral_restr0.0820.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022044
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 316 -
Rwork0.305 5211 -
all-5527 -
obs--99.87 %
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)
10.28290.1353-0.16940.8126-0.17821.65470.0234-0.02320.07110.091-0.02820.0364-0.104-0.17630.00480.15840.01420.04860.0268-0.00940.033411.951326.034944.211
20.2677-0.11060.12220.7475-0.14551.58060.03180.0029-0.05-0.0786-0.0260.02880.1319-0.1138-0.00580.1799-0.01190.02290.0104-0.00330.014615.1558.06898.9739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 1301
2X-RAY DIFFRACTION2B6 - 1601

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