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- PDB-9eu4: GH29A alpha-L-fucosidase -

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Basic information

Entry
Database: PDB / ID: 9eu4
TitleGH29A alpha-L-fucosidase
ComponentsExported alpha-L-fucosidase protein
KeywordsHYDROLASE / GH29A / GH29 / fucosidase / fucose
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome
Similarity search - Function
Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-L-fucopyranose / Exported alpha-L-fucosidase protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsYang, Y.Y. / Zeuner, B. / Morth, J.P.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Independent Research Fund Denmark - Technology and Production Sciences1134-00002B Denmark
Other government202108320321
Citation
Journal: Febs J. / Year: 2025
Title: Structural elucidation and characterization of GH29A alpha-l-fucosidases and the effect of pH on their transglycosylation.
Authors: Yang, Y. / Holck, J. / Thorhallsson, A.T. / Hunt, C.J. / Yang, H. / Morth, J.P. / Meyer, A.S. / Zeuner, B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exported alpha-L-fucosidase protein
B: Exported alpha-L-fucosidase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5906
Polymers97,0692
Non-polymers5204
Water3,639202
1
A: Exported alpha-L-fucosidase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7953
Polymers48,5351
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exported alpha-L-fucosidase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7953
Polymers48,5351
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.372, 140.372, 110.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Exported alpha-L-fucosidase protein


Mass: 48534.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: BF9343_3156 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5LAD6
#2: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.15M Ammonium sulphate 0.1M Bis-tris pH 8.0 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.33→70.19 Å / Num. obs: 54083 / % possible obs: 98.19 % / Redundancy: 20.7 % / Biso Wilson estimate: 79.38 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1037 / Rpim(I) all: 0.02383 / Rrim(I) all: 0.1065 / Net I/σ(I): 14.42
Reflection shellResolution: 2.33→2.413 Å / Redundancy: 21.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 5354 / CC1/2: 0.337 / CC star: 0.71 / Rpim(I) all: 0.8767 / Rrim(I) all: 1 / % possible all: 82.36

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→70.19 Å / SU ML: 0.4906 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2322 2600 4.89 %
Rwork0.1907 50521 -
obs0.1929 53121 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.47 Å2
Refinement stepCycle: LAST / Resolution: 2.33→70.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 32 202 6892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826880
X-RAY DIFFRACTIONf_angle_d0.96949341
X-RAY DIFFRACTIONf_chiral_restr0.0543977
X-RAY DIFFRACTIONf_plane_restr0.00821196
X-RAY DIFFRACTIONf_dihedral_angle_d5.5998893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.370.431030.43761859X-RAY DIFFRACTION69.72
2.37-2.420.43611400.40762616X-RAY DIFFRACTION96.26
2.42-2.470.37871340.36892655X-RAY DIFFRACTION99.75
2.47-2.520.38611340.35542686X-RAY DIFFRACTION100
2.52-2.580.32221100.33122699X-RAY DIFFRACTION100
2.58-2.640.33071450.28632688X-RAY DIFFRACTION99.93
2.64-2.720.27961400.28512652X-RAY DIFFRACTION100
2.72-2.80.32041250.26942715X-RAY DIFFRACTION99.96
2.8-2.890.34151380.30432702X-RAY DIFFRACTION100
2.89-2.990.4341390.32742688X-RAY DIFFRACTION100
2.99-3.110.35651360.28342694X-RAY DIFFRACTION100
3.11-3.250.29941480.25052705X-RAY DIFFRACTION100
3.25-3.420.27221410.21792678X-RAY DIFFRACTION100
3.42-3.640.25871320.20982718X-RAY DIFFRACTION99.93
3.64-3.920.22891350.17642717X-RAY DIFFRACTION100
3.92-4.310.1771480.14642710X-RAY DIFFRACTION100
4.31-4.930.17631590.12992728X-RAY DIFFRACTION99.97
4.93-6.210.21761510.15172752X-RAY DIFFRACTION100
6.22-70.190.17411420.15642859X-RAY DIFFRACTION99.6
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)
12.56669342561.434666914820.3687177048583.5619053926-0.5049109708440.852223246788-0.146157721101-0.06383836329240.376736261116-0.8970340927390.1136359183010.9121255539540.267643911841-0.1074927021930.00071117597021.090461080350.0886902275015-0.2785207891060.748080333994-0.153521871490.74342432725320.117988534455.172681222327.9804574643
20.7945045324230.142572658124-0.85551641651.48487987943-1.032775431991.45868679910.00824761196854-0.0992346075465-0.294152608295-0.63536062716-0.1353876479880.1273521394680.2538505403520.1658051838790.000357899773131.007645291210.0973974844263-0.09109609050180.727766208191-0.1255590811320.74808626514324.245743256935.237263682437.0404791879
30.5822023329510.608773867634-0.5713612003820.892841022992-0.1834397695311.224587652710.08582546812420.00794619300112-0.688472885756-0.336540973384-0.09059409908530.2220164663230.503999020976-0.26476510297-0.001693757029150.965656493511-0.0300571637758-0.1644807062920.774341542706-0.08465374517431.2768231622912.841279249617.213105768145.2916027228
42.08058926276-0.502789906609-0.3376748966743.18264253103-0.2534405457361.68656242442-0.0364820548609-0.3585964539480.05174914232390.668516502855-0.269984492443-0.794429509609-0.2287640119360.258499907549-0.002097541283580.817442879996-0.215527245693-0.3269327930850.8585370856660.1415204127020.808408663899-11.386925504257.0942876175.82237592587
52.55819321512-0.262544777794-0.6769593586552.73199705209-0.6108891622031.861164246780.07977232522310.08137700992720.0582004940897-0.145097240643-0.280813741641-1.24888236414-0.01854372197350.303365603301-0.007791857957220.672433930115-0.147524613724-0.186677942731.008839333380.254531651071.26469441893-2.8042747043358.193960126-5.61075964846
60.0325387699760.144065759697-0.1061411868082.270394533970.922709408621.87273769034-0.0453795221066-0.243039958275-0.4182636682810.260961312082-0.402826117267-0.4073773003250.2012894962850.2765034249763.19747996766E-50.693003955737-0.01167496581680.06175347257130.752611980460.2632314790651.02382416243-11.15119924928.6921178765-3.67825694645
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 281 )AA23 - 2811 - 259
22chain 'A' and (resid 282 through 376 )AA282 - 376260 - 354
33chain 'A' and (resid 377 through 435 )AA377 - 435355 - 413
44chain 'B' and (resid 23 through 162 )BC23 - 1621 - 140
55chain 'B' and (resid 163 through 281 )BC163 - 281141 - 259
66chain 'B' and (resid 282 through 434 )BC282 - 434260 - 412

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