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- PDB-7snk: Structure of Bacple_01702, a GH29 family glycoside hydrolase -

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Basic information

Entry
Database: PDB / ID: 7snk
TitleStructure of Bacple_01702, a GH29 family glycoside hydrolase
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / GH29 family / bacterial glycoside hydrolase
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome / metal ion binding
Similarity search - Function
Alpha-L-fucosidase, C-terminal / Alpha-L-fucosidase C-terminal domain / Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / Alpha-L-fucosidase
Similarity search - Component
Biological speciesPhocaeicola plebeius DSM 17135 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUlaganathan, T. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biorxiv / Year: 2023
Title: The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations
Authors: Mathieu, S. / Touvrey, M. / Poulet, L. / Drouillard, S. / Ulaganathan, T.S. / Segurel, L. / Cygler, M. / Helbert, W.
History
DepositionOct 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2694
Polymers68,0401
Non-polymers2293
Water7,891438
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.450, 77.430, 133.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

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Components

#1: Protein Alpha-L-fucosidase


Mass: 68040.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola plebeius DSM 17135 (bacteria)
Gene: BACPLE_01702
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B5CYA5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% Peg8K, 0.1M Potassium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→44.54 Å / Num. obs: 38905 / % possible obs: 99.6 % / Redundancy: 23.8 % / Biso Wilson estimate: 30.27 Å2 / CC1/2: 0.99 / Net I/σ(I): 22.2
Reflection shellResolution: 2→2.11 Å / Mean I/σ(I) obs: 5.11 / Num. unique obs: 5643 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
PHENIXphasing
Cootmodel building
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NI3

4ni3


Resolution: 2→44.54 Å / SU ML: 0.2207 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.0197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 1944 5 %
Rwork0.1704 36926 -
obs0.1725 38870 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.3 Å2
Refinement stepCycle: LAST / Resolution: 2→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 11 438 4966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754655
X-RAY DIFFRACTIONf_angle_d0.84116325
X-RAY DIFFRACTIONf_chiral_restr0.0544662
X-RAY DIFFRACTIONf_plane_restr0.0067811
X-RAY DIFFRACTIONf_dihedral_angle_d6.1352614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2921360.24042582X-RAY DIFFRACTION99.02
2.05-2.110.25441370.20712597X-RAY DIFFRACTION99.17
2.11-2.170.28291350.19342572X-RAY DIFFRACTION99.27
2.17-2.240.21491360.1862572X-RAY DIFFRACTION99.41
2.24-2.320.24131380.1912626X-RAY DIFFRACTION99.39
2.32-2.410.25791380.19732609X-RAY DIFFRACTION99.53
2.41-2.520.26151360.18922595X-RAY DIFFRACTION99.27
2.52-2.650.22231370.18952621X-RAY DIFFRACTION99.71
2.65-2.820.24451390.1862630X-RAY DIFFRACTION99.75
2.82-3.040.26971400.19882655X-RAY DIFFRACTION99.75
3.04-3.340.22251380.17372639X-RAY DIFFRACTION99.89
3.34-3.830.19541420.15532679X-RAY DIFFRACTION99.93
3.83-4.820.15241430.12662717X-RAY DIFFRACTION99.97
4.82-44.540.18271490.16062832X-RAY DIFFRACTION99.8
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)
10.344393982827-0.143485547181-0.1505922661920.962363737960.0459531416381.17673850036-0.061026065262-0.04945814547-0.004012660226120.1457842380440.08151783418210.01757873885780.09916643336440.1068540178470.0002109557028580.1965591795180.0282119916915-0.009932720757830.192811627666-0.001685328640360.17968707141915.644776499416.12659815619.9211852836
20.4914697734170.0249376940879-0.2616858375370.3667152443710.313603866750.442220538195-0.011146218270.089120365222-0.122319875063-0.1288995226360.0185659249593-0.06087979877230.1073817835140.1161849400364.22060257014E-60.2034225523070.004599580021270.01743652041840.208591441598-0.01783493600920.21428889128518.322197598918.872839576-11.0970940347
30.40282705293-0.02351111476010.00710636680170.1400722396370.08645320780380.350575168764-0.08198054097730.148230520373-0.105305746268-0.1544382307280.04429152644390.1519024106170.219773591312-0.171710081868-4.73541387319E-50.258245100267-0.0737650209217-0.004214220880470.262812280191-0.01565088518710.305432521548-7.3692683577517.8740990809-15.1580372974
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 329 )26 - 3291 - 304
22chain 'A' and (resid 330 through 501 )330 - 501305 - 470
33chain 'A' and (resid 502 through 595 )502 - 595471 - 564

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