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- PDB-6o1i: Alpha-L-fucosidase AlfC fucosyltransferase mutant E274A -

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Basic information

Entry
Database: PDB / ID: 6o1i
TitleAlpha-L-fucosidase AlfC fucosyltransferase mutant E274A
ComponentsAlfC
KeywordsHYDROLASE / Fucosidase / fucosyltransferase / AlfC
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 / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Alpha-L-fucosidase / Alpha-L-fucosidase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.55 Å
AuthorsKlontz, E.H. / Sundberg, E.J.
CitationJournal: Nat Commun / Year: 2020
Title: Structure and dynamics of an alpha-fucosidase reveal a mechanism for highly efficient IgG transfucosylation.
Authors: Klontz, E.H. / Li, C. / Kihn, K. / Fields, J.K. / Beckett, D. / Snyder, G.A. / Wintrode, P.L. / Deredge, D. / Wang, L.X. / Sundberg, E.J.
History
DepositionFeb 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AlfC
B: AlfC
C: AlfC
D: AlfC


Theoretical massNumber of molelcules
Total (without water)157,2474
Polymers157,2474
Non-polymers00
Water00
1
A: AlfC
C: AlfC

A: AlfC
C: AlfC


Theoretical massNumber of molelcules
Total (without water)157,2474
Polymers157,2474
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
B: AlfC
D: AlfC

B: AlfC
D: AlfC


Theoretical massNumber of molelcules
Total (without water)157,2474
Polymers157,2474
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)87.753, 139.300, 265.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA2 - 3452 - 345
21LEULEUBB2 - 3452 - 345
12LEULEUAA2 - 3452 - 345
22LEULEUCC2 - 3452 - 345
13ARGARGAA2 - 3442 - 344
23ARGARGDD2 - 3442 - 344
14LEULEUBB2 - 3452 - 345
24LEULEUCC2 - 3452 - 345
15ARGARGBB2 - 3442 - 344
25ARGARGDD2 - 3442 - 344
16ARGARGCC2 - 3442 - 344
26ARGARGDD2 - 3442 - 344

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
AlfC


Mass: 39311.715 Da / Num. of mol.: 4 / Mutation: E274A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: K0NB39, UniProt: A0A422MHI3*PLUS, alpha-L-fucosidase

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 250 nL 20 mg/mL AlfC + 250 nL mother liquor (18% w/v PEG3350, 0.1 M Bis-Tris propane, pH 7, 20 mM sodium/potassium phosphate, 1% v/v glycerol), crystals appeared after five days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920099 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 14, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920099 Å / Relative weight: 1
ReflectionResolution: 3.55→29.12 Å / Num. obs: 18262 / % possible obs: 91.8 % / Redundancy: 4.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.094 / Rrim(I) all: 0.222 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.55-3.8951.99343830.350.9132.293.6
8.7-29.125.10.03612560.9980.0170.0487.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O18

6o18


Resolution: 3.55→29.12 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.919 / SU B: 108.439 / SU ML: 0.662 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.747
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 914 5 %RANDOM
Rwork0.2463 ---
obs0.2471 17348 90.8 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 243.13 Å2 / Biso mean: 94.67 Å2 / Biso min: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å2-0 Å2
2--1.27 Å20 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 3.55→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10197 0 0 0 10197
Num. residues----1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310486
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178934
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.63714274
X-RAY DIFFRACTIONr_angle_other_deg1.1631.57620728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39451288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60924.021562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.667151557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.411532
X-RAY DIFFRACTIONr_chiral_restr0.0350.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022294
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A111330.01
12B111330.01
21A111080.03
22C111080.03
31A110490.04
32D110490.04
41B110490.03
42C110490.03
51B110240.04
52D110240.04
61C109640.04
62D109640.04
LS refinement shellResolution: 3.55→3.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 66 -
Rwork0.371 1289 -
all-1355 -
obs--93.32 %
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)
14.9636-1.7346-1.06233.0913-0.69955.17270.31220.36381.18740.03490.3020.1603-1.60670.2167-0.61421.0104-0.18250.27320.230.07220.556128.74924.223-5.705
23.1482-0.6521-1.37912.30890.94997.51090.4217-1.0503-0.33620.19940.1786-0.63470.3311.9554-0.60020.6078-0.1942-0.13420.82380.02590.320654.21415.045-43.735
32.61440.23680.05332.1266-0.21494.35240.0145-1.0239-0.1470.77730.49041.0059-0.0311-0.9805-0.50490.94440.36590.52620.92370.27140.84838.1376.19224.315
43.3678-0.4970.1623.2306-1.55735.32890.76110.03810.3509-0.11420.21180.7855-2.2107-2.4097-0.9731.68060.87430.54861.35470.23310.417321.636.172-55.612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 345
2X-RAY DIFFRACTION2B2 - 345
3X-RAY DIFFRACTION3C2 - 345
4X-RAY DIFFRACTION4D2 - 344

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