[English] 日本語
Yorodumi
- PDB-6ohe: Alpha-L-fucosidase AlfC D200A in complex with Fuca(1,6)GlcNAc -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 3.14 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more