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- PDB-7znz: Crystal structure of unliganded form of FucOB, a GH95 family alph... -

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Basic information

Entry
Database: PDB / ID: 7znz
TitleCrystal structure of unliganded form of FucOB, a GH95 family alpha-1,2-fucosidase from Akkermansia muciniphila
ComponentsFucOB, a GH95 family alpha-1,2-fucosidase
KeywordsHYDROLASE / Gut microbiota Glycosyl hydrolase Fucosidase Mucin Bombay blood group Blood conversion
Function / homology
Function and homology information


alpha-L-fucosidase activity / carbohydrate metabolic process
Similarity search - Function
Alpha-L-fucosidase / : / : / Glycoside hydrolase family 95, C-terminal domain / Glycosyl hydrolase family 95 catalytic domain / Glycosyl hydrolase family 95, N-terminal domain / Glycosyl hydrolase family 65, N-terminal domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAnso, I. / Cifuente, J.O. / Trastoy, B. / Guerin, M.E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO) Spain
CitationJournal: Nat Commun / Year: 2023
Title: Turning universal O into rare Bombay type blood.
Authors: Anso, I. / Naegeli, A. / Cifuente, J.O. / Orrantia, A. / Andersson, E. / Zenarruzabeitia, O. / Moraleda-Montoya, A. / Garcia-Alija, M. / Corzana, F. / Del Orbe, R.A. / Borrego, F. / Trastoy, ...Authors: Anso, I. / Naegeli, A. / Cifuente, J.O. / Orrantia, A. / Andersson, E. / Zenarruzabeitia, O. / Moraleda-Montoya, A. / Garcia-Alija, M. / Corzana, F. / Del Orbe, R.A. / Borrego, F. / Trastoy, B. / Sjogren, J. / Guerin, M.E.
History
DepositionApr 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: FucOB, a GH95 family alpha-1,2-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6965
Polymers84,3281
Non-polymers3684
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-2 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.670, 100.400, 156.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FucOB, a GH95 family alpha-1,2-fucosidase


Mass: 84327.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Strain: ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc
Gene: Amuc_1120 / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UR61
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM potassium fluoride, 20% (w/v) PEG 3500 (PEG ION HR2-126 protein crystallization screen, Hampton Research)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→47.81 Å / Num. obs: 152310 / % possible obs: 99.95 % / Redundancy: 13 % / Biso Wilson estimate: 33.17 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05009 / Rpim(I) all: 0.01443 / Rrim(I) all: 0.05216 / Net I/σ(I): 32.63
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.5504 / Mean I/σ(I) obs: 4.82 / Num. unique obs: 6192 / CC1/2: 0.959 / CC star: 0.99 / Rpim(I) all: 0.1601 / Rrim(I) all: 0.5735 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EAB

2eab


Resolution: 1.8→47.81 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 7612 5 %
Rwork0.1885 144698 -
obs0.1899 152310 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.16 Å2 / Biso mean: 43.1067 Å2 / Biso min: 20.55 Å2
Refinement stepCycle: final / Resolution: 1.8→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5811 0 24 422 6257
Biso mean--50.81 45.48 -
Num. residues----761
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.820.3552310.355456096
1.82-1.840.36992570.32844870100
1.84-1.860.33442530.30744874100
1.86-1.880.32242550.29914790100
1.88-1.910.28922620.28394852100
1.91-1.940.32822540.29174832100
1.94-1.960.26392550.26174805100
1.96-1.990.27652520.24834835100
1.99-2.020.30842510.24624813100
2.02-2.060.2712550.23164853100
2.06-2.090.27172490.22654832100
2.09-2.130.26542540.21574813100
2.13-2.170.21362550.21364826100
2.17-2.220.2652580.20924837100
2.22-2.260.29772520.22954831100
2.26-2.320.22112540.20694821100
2.32-2.370.25942580.20354860100
2.37-2.440.24532580.18974853100
2.44-2.510.2142500.19624785100
2.51-2.590.22352530.19134860100
2.59-2.680.23912580.18724841100
2.68-2.790.2032570.18584805100
2.79-2.920.24432520.19124841100
2.92-3.070.25262540.19684838100
3.07-3.270.22772570.20214827100
3.27-3.520.22062570.18514831100
3.52-3.870.22530.1694827100
3.87-4.430.17022580.14494815100
4.43-5.580.13262450.13264834100
5.58-47.810.18952550.1744837100

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