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- PDB-6o1a: Alpha-L-fucosidase AlfC from Lactobacillus casei in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6o1a
TitleAlpha-L-fucosidase AlfC from Lactobacillus casei in complex with alpha-L-fucose product
ComponentsAlfC
KeywordsHYDROLASE / Fucosidase / product / fucose
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process
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 / Alpha-L-fucosidase / Alpha-L-fucosidase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 16, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 1.3Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1368
Polymers157,4794
Non-polymers6574
Water23413
1
A: AlfC
C: AlfC
hetero molecules

A: AlfC
C: AlfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1368
Polymers157,4794
Non-polymers6574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
B: AlfC
D: AlfC
hetero molecules

B: AlfC
D: AlfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1368
Polymers157,4794
Non-polymers6574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Unit cell
Length a, b, c (Å)89.983, 138.236, 264.440
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: 0 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA4 - 3444 - 344
21ARGARGBB4 - 3444 - 344
12LEULEUAA2 - 3452 - 345
22LEULEUCC2 - 3452 - 345
13ARGARGAA2 - 3442 - 344
23ARGARGDD2 - 3442 - 344
14ARGARGBB4 - 3444 - 344
24ARGARGCC4 - 3444 - 344
15ASNASNBB4 - 3434 - 343
25ASNASNDD4 - 3434 - 343
16ARGARGCC2 - 3442 - 344
26ARGARGDD2 - 3442 - 344

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
AlfC


Mass: 39369.750 Da / Num. of mol.: 4
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
#2: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 250 nL 20 mg/mL wild-type 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, ...Details: 250 nL 20 mg/mL wild-type 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, were harvested in mother liquor + 20% v/v glycerol + 10 mM alpha-L-fucose for ~1 minute, then flash-cooled

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2017
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 2.6→29.84 Å / Num. obs: 50905 / % possible obs: 99.7 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.028 / Rrim(I) all: 0.063 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.6-2.685.11.29243900.4840.6191.437100
10.72-29.824.50.0357590.9980.0170.03993.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O18

6o18


Resolution: 2.6→29.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 35.369 / SU ML: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.65 / ESU R Free: 0.276
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 2486 4.9 %RANDOM
Rwork0.2078 ---
obs0.2087 48372 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 212.23 Å2 / Biso mean: 101.99 Å2 / Biso min: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å20 Å2
2---1.92 Å2-0 Å2
3---2.77 Å2
Refinement stepCycle: final / Resolution: 2.6→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10198 0 44 13 10255
Biso mean--102.09 96.79 -
Num. residues----1291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01310531
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178911
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.64214343
X-RAY DIFFRACTIONr_angle_other_deg1.2621.58120712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59451283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37224.378571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.214151559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4191528
X-RAY DIFFRACTIONr_chiral_restr0.0560.21332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022273
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A107660.06
12B107660.06
21A108550.07
22C108550.07
31A107010.07
32D107010.07
41B107340.06
42C107340.06
51B105900.06
52D105900.06
61C106400.07
62D106400.07
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 177 -
Rwork0.367 3580 -
all-3757 -
obs--99.76 %
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)
13.7258-0.90110.63472.5950.18782.43180.07680.3565-1.1271-0.15690.2131-0.11580.6606-0.1054-0.28980.3868-0.1237-0.08440.1579-0.09260.4636-29.297-24.195-5.824
22.0869-0.38730.98472.2743-0.4266.11630.3817-0.72160.26660.2360.1690.3111-0.7007-1.5934-0.55070.43950.01270.18860.61510.04290.1678-55.017-15.189-43.235
33.68740.2955-0.20641.345-0.04133.26840.0003-1.1965-0.07590.50030.2889-0.5527-0.00610.4557-0.28930.410.1768-0.25420.6763-0.08940.3465-8.994-6.35724.088
42.2386-0.39130.10612.83060.59015.09220.53320.0035-0.0987-0.09250.1191-0.79071.15071.8931-0.65230.65450.4026-0.20530.8586-0.24390.3155-22.574-35.187-55.079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 345
2X-RAY DIFFRACTION2B4 - 344
3X-RAY DIFFRACTION3C2 - 345
4X-RAY DIFFRACTION4D2 - 344

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