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- PDB-7zo0: Crystal structure of catalytic inactive unliganded form of FucOB,... -

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Basic information

Entry
Database: PDB / ID: 7zo0
TitleCrystal structure of catalytic inactive unliganded form of FucOB, a GH95 family alpha-1,2-fucosidase from Akkermansia muciniphila
ComponentsGH95 family alpha-1,2-fucosidase
KeywordsHYDROLASE / Glycosyl hydrolase Fucosidase Akkermansia muciniphila 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: 1.95 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: GH95 family alpha-1,2-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8436
Polymers87,3831
Non-polymers4605
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-3 kcal/mol
Surface area25970 Å2
Unit cell
Length a, b, c (Å)53.582, 87.507, 95.586
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 87382.805 Da / Num. of mol.: 1 / Mutation: E541A
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 (E. coli) / References: UniProt: B2UR61
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM sodium chloride, 20% (w/v) PEG 3350 (PEG ION suite protein crystallization screening, Hampton Research)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.95→52.24 Å / Num. obs: 423928 / % possible obs: 99.84 % / Redundancy: 6.8 % / Biso Wilson estimate: 27.38 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1299 / Rpim(I) all: 0.05409 / Rrim(I) all: 0.1409 / Net I/σ(I): 12.84
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 43184 / CC1/2: 0.648 / CC star: 0.887 / Rpim(I) all: 0.4985 / Rrim(I) all: 1.323 / % possible all: 99.77

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZNZ

7znz


Resolution: 1.95→52.24 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 2959 4.71 %
Rwork0.2036 --
obs0.2041 62844 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→52.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5719 0 30 252 6001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045913
X-RAY DIFFRACTIONf_angle_d0.6228048
X-RAY DIFFRACTIONf_dihedral_angle_d15.32074
X-RAY DIFFRACTIONf_chiral_restr0.045845
X-RAY DIFFRACTIONf_plane_restr0.0031059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.35721290.31182835X-RAY DIFFRACTION99
1.98-2.010.30191560.27942792X-RAY DIFFRACTION100
2.01-2.050.28211450.26972842X-RAY DIFFRACTION100
2.05-2.090.31091400.26592833X-RAY DIFFRACTION100
2.09-2.130.27471140.2522878X-RAY DIFFRACTION100
2.13-2.180.23771300.24182862X-RAY DIFFRACTION100
2.18-2.230.26721330.24642872X-RAY DIFFRACTION100
2.23-2.290.28551330.25092802X-RAY DIFFRACTION100
2.29-2.350.23441530.23152852X-RAY DIFFRACTION100
2.35-2.420.24081530.22272800X-RAY DIFFRACTION100
2.42-2.490.2141330.22052868X-RAY DIFFRACTION100
2.49-2.580.23061370.21882875X-RAY DIFFRACTION100
2.58-2.690.25521270.23432857X-RAY DIFFRACTION100
2.69-2.810.29311270.21682865X-RAY DIFFRACTION100
2.81-2.960.21941600.21982840X-RAY DIFFRACTION100
2.96-3.140.21591430.20772847X-RAY DIFFRACTION100
3.14-3.380.18181290.19322873X-RAY DIFFRACTION100
3.38-3.720.1781660.1812835X-RAY DIFFRACTION100
3.73-4.260.16981530.1632859X-RAY DIFFRACTION100
4.26-5.370.18831500.15792878X-RAY DIFFRACTION100
5.37-52.240.17161480.17652920X-RAY DIFFRACTION100

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