[English] 日本語
Yorodumi
- PDB-6o18: Unliganded alpha-L-fucosidase AlfC from Lactobacillus casei -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o18
TitleUnliganded alpha-L-fucosidase AlfC from Lactobacillus casei
ComponentsAlfC
KeywordsHYDROLASE / Fucosidase / apo
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 / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)157,4794
Polymers157,4794
Non-polymers00
Water59433
1
A: AlfC
C: AlfC

A: AlfC
C: AlfC


Theoretical massNumber of molelcules
Total (without water)157,4794
Polymers157,4794
Non-polymers00
Water724
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)157,4794
Polymers157,4794
Non-polymers00
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)89.298, 137.119, 264.709
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 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEUAA3 - 3453 - 345
21ASPASPLEULEUBB3 - 3453 - 345
12ASNASNLEULEUAA2 - 3452 - 345
22ASNASNLEULEUCC2 - 3452 - 345
13ASNASNARGARGAA2 - 3442 - 344
23ASNASNARGARGDD2 - 3442 - 344
14ASPASPLEULEUBB3 - 3453 - 345
24ASPASPLEULEUCC3 - 3453 - 345
15ASPASPASNASNBB3 - 3433 - 343
25ASPASPASNASNDD3 - 3433 - 343
16ASNASNARGARGCC2 - 3442 - 344
26ASNASNARGARGDD2 - 3442 - 344

NCS ensembles :
ID
1
2
3
4
5
6

-
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
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/potassion phosphate, 1% v/v glycerol), crystals appeared after five days

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.55→29.41 Å / Num. obs: 53160 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.029 / Rrim(I) all: 0.069 / Net I/σ(I): 12.7 / Num. measured all: 291121 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.55-2.635.51.25645660.5570.581.387100
10.51-29.415.10.0378050.9980.0170.0495

-
Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PCT

4pct


Resolution: 2.55→29.11 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 30.369 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.557 / ESU R Free: 0.283
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 2621 4.9 %RANDOM
Rwork0.2079 ---
obs0.2096 50495 99.57 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 187.67 Å2 / Biso mean: 91.322 Å2 / Biso min: 52.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2---4.59 Å2-0 Å2
3---2.57 Å2
Refinement stepCycle: final / Resolution: 2.55→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10192 0 0 33 10225
Biso mean---79.31 -
Num. residues----1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310483
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178857
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.63614285
X-RAY DIFFRACTIONr_angle_other_deg1.3341.57520546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06451292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04824.196560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.452151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1761529
X-RAY DIFFRACTIONr_chiral_restr0.0620.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022284
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110190.06
12B110190.06
21A110680.07
22C110680.07
31A109590.07
32D109590.07
41B109820.06
42C109820.06
51B108420.07
52D108420.07
61C108490.08
62D108490.08
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 195 -
Rwork0.351 3677 -
all-3872 -
obs--99.69 %
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)
13.1376-0.69810.49372.27390.06562.41740.11280.3474-0.9489-0.1540.1438-0.0110.6347-0.0119-0.25670.3087-0.0653-0.08650.1795-0.07720.339-29.398-24.033-5.601
21.7953-0.09550.26681.9635-0.49194.48070.32-0.46230.31810.28960.13370.3411-0.5135-0.9734-0.45380.3046-0.01290.16130.4356-0.0080.1688-54.819-14.88-43.69
33.01750.1598-0.34541.6429-0.23822.6405-0.017-0.92370.0830.45920.1519-0.4867-0.11380.551-0.1350.35240.0986-0.24020.6299-0.05850.246-9.019-6.17623.883
41.9805-0.1309-0.36762.53290.73773.53920.3464-0.1528-0.12230.00760.1067-0.70550.80061.3496-0.45310.47740.2865-0.17350.6754-0.12860.2601-22.307-34.917-55.331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 345
2X-RAY DIFFRACTION2B3 - 345
3X-RAY DIFFRACTION3C2 - 345
4X-RAY DIFFRACTION4D2 - 344

+
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