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- PDB-6ohe: Alpha-L-fucosidase AlfC D200A in complex with Fuca(1,6)GlcNAc -

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Basic information

Entry
Database: PDB / ID: 6ohe
TitleAlpha-L-fucosidase AlfC D200A in complex with Fuca(1,6)GlcNAc
ComponentsAlfC
KeywordsHYDROLASE / Fucosidase / AlfC / Fuca(1 / 6)GlcNAc
Function / homologyAlpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / alpha-L-fucosidase activity / fucose metabolic process / Glycoside hydrolase superfamily / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.14 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
DepositionApr 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 16, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)158,7728
Polymers157,3034
Non-polymers1,4694
Water00
1
A: AlfC
C: AlfC
hetero molecules

A: AlfC
C: AlfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,7728
Polymers157,3034
Non-polymers1,4694
Water0
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)158,7728
Polymers157,3034
Non-polymers1,4694
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)89.022, 139.251, 263.375
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
11(chain A and (resseq 4:244 or resseq 267:345 or (resid...
21(chain B and (resseq 4:244 or resseq 267:345 or (resid...
31(chain C and (resseq 4:244 or resseq 267:345 or (resid...
41(chain D and (resseq 4:244 or resseq 267:345 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 4:244 or resseq 267:345 or (resid...A4 - 244
121(chain A and (resseq 4:244 or resseq 267:345 or (resid...A267 - 345
131(chain A and (resseq 4:244 or resseq 267:345 or (resid...A2 - 345
141(chain A and (resseq 4:244 or resseq 267:345 or (resid...A2 - 345
151(chain A and (resseq 4:244 or resseq 267:345 or (resid...A2 - 345
161(chain A and (resseq 4:244 or resseq 267:345 or (resid...A2 - 345
171(chain A and (resseq 4:244 or resseq 267:345 or (resid...A2 - 345
181(chain A and (resseq 4:244 or resseq 267:345 or (resid...A2 - 345
191(chain A and (resseq 4:244 or resseq 267:345 or (resid...A2 - 345
1101(chain A and (resseq 4:244 or resseq 267:345 or (resid...A2 - 345
1111(chain A and (resseq 4:244 or resseq 267:345 or (resid...A2 - 345
211(chain B and (resseq 4:244 or resseq 267:345 or (resid...B4 - 244
221(chain B and (resseq 4:244 or resseq 267:345 or (resid...B267 - 345
231(chain B and (resseq 4:244 or resseq 267:345 or (resid...B346
241(chain B and (resseq 4:244 or resseq 267:345 or (resid...B3 - 345
251(chain B and (resseq 4:244 or resseq 267:345 or (resid...B3 - 345
261(chain B and (resseq 4:244 or resseq 267:345 or (resid...B3 - 345
271(chain B and (resseq 4:244 or resseq 267:345 or (resid...B3 - 345
281(chain B and (resseq 4:244 or resseq 267:345 or (resid...B3 - 345
311(chain C and (resseq 4:244 or resseq 267:345 or (resid...C4 - 244
321(chain C and (resseq 4:244 or resseq 267:345 or (resid...C267 - 345
331(chain C and (resseq 4:244 or resseq 267:345 or (resid...C346
341(chain C and (resseq 4:244 or resseq 267:345 or (resid...C4 - 345
351(chain C and (resseq 4:244 or resseq 267:345 or (resid...C4 - 345
361(chain C and (resseq 4:244 or resseq 267:345 or (resid...C4 - 345
371(chain C and (resseq 4:244 or resseq 267:345 or (resid...C4 - 345
381(chain C and (resseq 4:244 or resseq 267:345 or (resid...C4 - 345
391(chain C and (resseq 4:244 or resseq 267:345 or (resid...C4 - 345
3101(chain C and (resseq 4:244 or resseq 267:345 or (resid...C4 - 345
411(chain D and (resseq 4:244 or resseq 267:345 or (resid...D4 - 244
421(chain D and (resseq 4:244 or resseq 267:345 or (resid...D267 - 345
431(chain D and (resseq 4:244 or resseq 267:345 or (resid...D346
441(chain D and (resseq 4:244 or resseq 267:345 or (resid...D4 - 345
451(chain D and (resseq 4:244 or resseq 267:345 or (resid...D4 - 345
461(chain D and (resseq 4:244 or resseq 267:345 or (resid...D4 - 345
471(chain D and (resseq 4:244 or resseq 267:345 or (resid...D4 - 345
481(chain D and (resseq 4:244 or resseq 267:345 or (resid...D4 - 345
491(chain D and (resseq 4:244 or resseq 267:345 or (resid...D4 - 345
4101(chain D and (resseq 4:244 or resseq 267:345 or (resid...D4 - 345

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Components

#1: Protein
AlfC


Mass: 39325.742 Da / Num. of mol.: 4 / Mutation: D200A
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: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 250 nL 20 mg/mL AlfC D200A + 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 AlfC D200A + 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, unliganded crystals were harvested in mother liquor supplemented with 20% v/v glycerol for cryoprotection and 10 mM Fuca(1,6)GlcNAc for ~1 minute, flash-cooled in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.14→29.76 Å / Num. obs: 28950 / % possible obs: 99.7 % / Redundancy: 5 % / Biso Wilson estimate: 88.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.092 / Rrim(I) all: 0.211 / Net I/σ(I): 6 / Num. measured all: 143330 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.14-3.334.91.56846240.4470.7751.75599.9
9.42-29.764.50.0711160.9940.0350.07995.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O18

6o18


Resolution: 3.14→29.76 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.68
RfactorNum. reflection% reflection
Rfree0.2986 1445 5 %
Rwork0.2785 --
obs0.2795 28900 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 211.14 Å2 / Biso mean: 126.6206 Å2 / Biso min: 50.71 Å2
Refinement stepCycle: final / Resolution: 3.14→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10267 0 100 0 10367
Biso mean--109.54 --
Num. residues----1289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710661
X-RAY DIFFRACTIONf_angle_d1.25914510
X-RAY DIFFRACTIONf_chiral_restr0.071516
X-RAY DIFFRACTIONf_plane_restr0.0061883
X-RAY DIFFRACTIONf_dihedral_angle_d12.5536173
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6103X-RAY DIFFRACTION9.486TORSIONAL
12B6103X-RAY DIFFRACTION9.486TORSIONAL
13C6103X-RAY DIFFRACTION9.486TORSIONAL
14D6103X-RAY DIFFRACTION9.486TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.14-3.25210.38351540.411526692823100
3.2521-3.38220.39661260.401327382864100
3.3822-3.53590.43681480.375727112859100
3.5359-3.72190.41381460.368827222868100
3.7219-3.95460.32721370.332227442881100
3.9546-4.25920.30311370.315327232860100
4.2592-4.68630.30071420.286627602902100
4.6863-5.3610.2851630.26527342897100
5.361-6.74130.26621420.251427852927100
6.7413-29.76380.21371500.18232869301999
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)
10.61-0.3454-0.34611.1257-0.35171.83970.3649-0.3985-0.6566-0.48650.48970.54051.77040.4307-0.57511.59150.2809-0.78730.9267-0.05811.1596-15.4622-24.59935.3634
22.2588-0.5773-0.54610.7858-0.2612.80810.52140.9764-0.0526-0.34360.0072-0.34510.22092.1619-0.41760.74730.1844-0.05591.7065-0.16670.674310.6272-15.464943.0927
31.15310.53660.310.26560.12242.32250.36580.7237-0.0177-0.43690.780.87340.6059-0.71590.05741.389-0.4164-1.06681.34040.58871.8469-35.1367-6.0561-24.6062
40.2844-0.19030.44960.42610.15451.42270.61550.3761-0.7099-0.20890.2548-0.60461.70631.5452-0.56071.80970.7162-0.96321.7434-0.38911.341722.0682-35.913377.5012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 2:345)A2 - 345
2X-RAY DIFFRACTION2(chain B and resseq 3:345)B2 - 345
3X-RAY DIFFRACTION3(chain C and resseq 4:345)C2 - 345
4X-RAY DIFFRACTION4(chain D and resseq 4:345)D2 - 345

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