[English] 日本語
Yorodumi
- PDB-8qf2: Beta-L-Arabinofurano-cyclitol Aziridines are Cysteine-directed Br... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qf2
TitleBeta-L-Arabinofurano-cyclitol Aziridines are Cysteine-directed Broad-spectrum Inhibitors and Activity-based Probes for Retaining Beta-L-arabinofuranosidases
ComponentsNon-reducing end beta-L-arabinofuranosidase
KeywordsHYDROLASE / arabinofuranosidase / activity-based probe / cyclophellitol aziridine
Function / homology
Function and homology information


non-reducing end beta-L-arabinofuranosidase / beta-L-arabinofuranosidase activity / polysaccharide catabolic process / metal ion binding
Similarity search - Function
: / : / Glycoside hydrolase family 127 C-terminal domain / Beta-L-arabinofuranosidase, GH127 / : / Beta-L-arabinofuranosidase, GH127 catalytic domain / Beta-L-arabinofuranosidase, GH127 middle domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Chem-UI5 / Non-reducing end beta-L-arabinofuranosidase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBorlandelli, V. / Offen, W.A. / Moroz, O. / Nin-Hill, A. / McGregor, N. / Binkhorst, L. / Armstrong, Z. / Ishiwata, A. / Artola, M. / Rovira, C. ...Borlandelli, V. / Offen, W.A. / Moroz, O. / Nin-Hill, A. / McGregor, N. / Binkhorst, L. / Armstrong, Z. / Ishiwata, A. / Artola, M. / Rovira, C. / Davies, G.J. / Overkleeft, H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: beta-l- Arabino furano-cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes for Retaining beta-l-Arabinofuranosidases.
Authors: Borlandelli, V. / Offen, W. / Moroz, O. / Nin-Hill, A. / McGregor, N. / Binkhorst, L. / Ishiwata, A. / Armstrong, Z. / Artola, M. / Rovira, C. / Davies, G.J. / Overkleeft, H.S.
History
DepositionSep 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-reducing end beta-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6703
Polymers74,4581
Non-polymers2132
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.260, 77.260, 254.647
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Non-reducing end beta-L-arabinofuranosidase


Mass: 74457.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GH127 beta-L-arabinofuranosidase HypBA1 with C-terminal His tag
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: hypBA1 / Production host: Escherichia coli (E. coli) / References: UniProt: E8MGH8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UI5 / (1~{S},2~{S},3~{S},4~{R})-4-azanyl-3-(hydroxymethyl)cyclopentane-1,2-diol


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.7 M sodium citrate, 0.1 M MES pH 6.5, 10 mM dithiothreitol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.35→85.03 Å / Num. obs: 37850 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.995 / Rmerge(I) obs: 0.199 / Net I/σ(I): 7.7
Reflection shellResolution: 2.35→2.43 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3624 / CC1/2: 0.66 / Rpim(I) all: 0.938 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→85.03 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.767 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS INSUFFICIENT ELECTRON DENSITY TO MODEL ASN44 AND GLN45.
RfactorNum. reflection% reflectionSelection details
Rfree0.25426 1886 5 %RANDOM
Rwork0.20685 ---
obs0.20933 35892 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.408 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20.82 Å2-0 Å2
2--1.63 Å20 Å2
3----5.3 Å2
Refinement stepCycle: 1 / Resolution: 2.35→85.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5096 0 11 74 5181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125231
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164711
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6647122
X-RAY DIFFRACTIONr_angle_other_deg0.4711.58210812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.304535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21510782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021233
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.1477.2482626
X-RAY DIFFRACTIONr_mcbond_other6.1447.2492626
X-RAY DIFFRACTIONr_mcangle_it8.26613.0163279
X-RAY DIFFRACTIONr_mcangle_other8.27113.0173280
X-RAY DIFFRACTIONr_scbond_it6.0887.2862605
X-RAY DIFFRACTIONr_scbond_other6.0877.2852606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3813.3493844
X-RAY DIFFRACTIONr_long_range_B_refined9.96866.475754
X-RAY DIFFRACTIONr_long_range_B_other9.96866.465755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 114 -
Rwork0.349 2614 -
obs--100 %

+
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