[English] 日本語
Yorodumi
- PDB-7kq4: Structure of isethionate sulfite-lyase from Bilophila wadsworthia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kq4
TitleStructure of isethionate sulfite-lyase from Bilophila wadsworthia with glycerol bound
ComponentsIsethionate sulfite-lyase
KeywordsLYASE / glycyl radical enzyme / isethionate-sulfite lyase / carbon-sulfur bond cleavage / microbiome
Function / homology
Function and homology information


isethionate sulfite-lyase / alkanesulfonate catabolic process / lyase activity / cytosol
Similarity search - Function
: / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
Isethionate sulfite-lyase
Similarity search - Component
Biological speciesBilophila wadsworthia
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.261 Å
AuthorsDawson, C.D. / Backman, L.R.F. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM069857 United States
CitationJournal: Cell Chem Biol / Year: 2021
Title: Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase.
Authors: Dawson, C.D. / Irwin, S.M. / Backman, L.R.F. / Le, C. / Wang, J.X. / Vennelakanti, V. / Yang, Z. / Kulik, H.J. / Drennan, C.L. / Balskus, E.P.
History
DepositionNov 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isethionate sulfite-lyase
B: Isethionate sulfite-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,3484
Polymers188,1632
Non-polymers1842
Water12,124673
1
A: Isethionate sulfite-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1742
Polymers94,0821
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isethionate sulfite-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1742
Polymers94,0821
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.064, 132.962, 107.934
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Isethionate sulfite-lyase / Glycyl radical enzyme IslA / GRE IslA


Mass: 94081.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bilophila wadsworthia (strain 3_1_6) (bacteria)
Strain: 3_1_6 / Gene: islA, iseG, HMPREF0179_00639 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5Y378, Lyases; Carbon-sulfur lyases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM calcium acetate, 15% w/v PEG 3350, and 3 mM sodium isethionate. Paraffin oil was used as a cryoprotectant.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 80740 / % possible obs: 98.4 % / Redundancy: 7.3 % / CC1/2: 0.989 / Net I/σ(I): 10.1
Reflection shellResolution: 2.26→2.34 Å / Num. unique obs: 6838 / CC1/2: 0.681

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FAU

5fau


Resolution: 2.261→49.223 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1975 3952 4.9 %
Rwork0.1637 76717 -
obs0.1653 80669 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.17 Å2 / Biso mean: 26.7612 Å2 / Biso min: 15.59 Å2
Refinement stepCycle: final / Resolution: 2.261→49.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13166 0 12 673 13851
Biso mean--23.29 28.29 -
Num. residues----1650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313512
X-RAY DIFFRACTIONf_angle_d0.59718298
X-RAY DIFFRACTIONf_dihedral_angle_d14.4228106
X-RAY DIFFRACTIONf_chiral_restr0.0441948
X-RAY DIFFRACTIONf_plane_restr0.0052398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.261-2.28850.25541010.225226982
2.2885-2.31750.26191230.2141265597
2.3175-2.3480.24891490.2099268599
2.348-2.38010.28381440.20382721100
2.3801-2.41410.23891520.19812741100
2.4141-2.45020.28221470.19112721100
2.4502-2.48850.24271480.18172705100
2.4885-2.52930.21031330.18172731100
2.5293-2.57290.26691280.17192764100
2.5729-2.61970.25381330.1732724100
2.6197-2.670.21431370.17232768100
2.67-2.72450.20441340.17022741100
2.7245-2.78380.21491730.16572708100
2.7838-2.84850.2311370.16362735100
2.8485-2.91970.16841410.15952747100
2.9197-2.99870.18751230.15962783100
2.9987-3.08690.18321490.15052746100
3.0869-3.18650.20441520.15452726100
3.1865-3.30040.17151330.15622768100
3.3004-3.43250.19651400.1552780100
3.4325-3.58870.19941470.15152761100
3.5887-3.77780.18161380.14662751100
3.7778-4.01440.17121470.13872783100
4.0144-4.32420.15511530.13662773100
4.3242-4.7590.17621390.14612818100
4.759-5.44690.16521480.15212805100
5.4469-6.85960.22641450.1822856100
6.8596-49.2230.16931580.1855295299

+
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