[English] 日本語
Yorodumi
- PDB-8ai4: Crystal structure of radical SAM epimerase EpeE C223A mutant from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ai4
TitleCrystal structure of radical SAM epimerase EpeE C223A mutant from Bacillus subtilis with [4Fe-4S] clusters, S-adenosyl-L-homocysteine and RiPP peptide 5 bound
Components
  • Putative exported peptide YydF
  • Radical SAM core domain-containing protein
KeywordsMETAL BINDING PROTEIN / radical SAM / metalloenzyme / iron-sulfur / RiPP
Function / homology
Function and homology information


iron-sulfur cluster binding / catalytic activity / metal ion binding
Similarity search - Function
YydF/SAG 2028 / Peptide radical SAM maturase , YydG / : / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / Peptide biosynthesis protein YydG / Putative exported peptide YydF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPolsinelli, I. / Fyfe, C.D. / Legrand, P. / Kubiak, X. / Chavas, L.M.G. / Berteau, O. / Benjdia, A.
Funding support France, European Union, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0014 France
European Research Council (ERC)617053European Union
Citation
Journal: Nat.Chem.Biol. / Year: 2024
Title: Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme.
Authors: Kubiak, X. / Polsinelli, I. / Chavas, L.M.G. / Fyfe, C.D. / Guillot, A. / Fradale, L. / Brewee, C. / Grimaldi, S. / Gerbaud, G. / Thureau, A. / Legrand, P. / Berteau, O. / Benjdia, A.
#1: Journal: Nat Chem / Year: 2017
Title: Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis.
Authors: Benjdia, A. / Guillot, A. / Ruffie, P. / Leprince, J. / Berteau, O.
History
DepositionJul 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Radical SAM core domain-containing protein
B: Radical SAM core domain-containing protein
C: Putative exported peptide YydF
D: Putative exported peptide YydF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,60134
Polymers82,6864
Non-polymers3,91530
Water9,944552
1
A: Radical SAM core domain-containing protein
C: Putative exported peptide YydF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,35217
Polymers41,3432
Non-polymers2,00915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-26 kcal/mol
Surface area15030 Å2
MethodPISA
2
B: Radical SAM core domain-containing protein
D: Putative exported peptide YydF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,25017
Polymers41,3432
Non-polymers1,90715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-29 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.37, 92.09, 126.43
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Radical SAM core domain-containing protein


Mass: 39920.379 Da / Num. of mol.: 2 / Mutation: C223A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_2355 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0A1MJP5
#2: Protein/peptide Putative exported peptide YydF


Mass: 1422.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) / References: UniProt: Q45596

-
Non-polymers , 6 types, 582 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 1000, Tris 0.1 M.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2021 / Details: KB mirrors
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.75→46.04 Å / Num. obs: 1406836 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.018 / Rrim(I) all: 0.069 / Net I/σ(I): 20.1
Reflection shellResolution: 1.75→1.8 Å / Rmerge(I) obs: 2.073 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 91475 / CC1/2: 0.518 / Rpim(I) all: 0.589 / Rrim(I) all: 2.157

-
Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fe-SAD experimental model

Resolution: 1.75→43.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.095 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.086
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 4700 -RANDOM
Rwork0.1727 ---
obs0.1736 93994 100 %-
Displacement parametersBiso mean: 43.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.0236 Å20 Å20 Å2
2--3.1274 Å20 Å2
3----1.1038 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.75→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5377 0 197 552 6126
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085877HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.97940HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2136SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1013HARMONIC5
X-RAY DIFFRACTIONt_it5877HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion761SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5786SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion15.32
LS refinement shellResolution: 1.75→1.76 Å
RfactorNum. reflection% reflection
Rfree0.2741 94 -
Rwork0.2934 --
obs0.2925 1880 100 %
Refinement TLS params.

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)
11.24030.1635-0.20890.6351-0.020.5433-0.00330.0158-0.02040.0158-0.0191-0.0198-0.0204-0.01980.02230.00030.0251-0.003-0.03740.0161-0.05091.3918-13.962-23.4159
21.5636-0.00580.68791.01830.11121.28220.0489-0.01790.0538-0.01790.0020.09970.05380.0997-0.0509-0.05470.01560.0296-0.0446-0.0124-0.038831.8839-27.9189-22.8671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 317
2X-RAY DIFFRACTION1{ A|* }A401 - 512
3X-RAY DIFFRACTION1{ A|* }A601 - 906
4X-RAY DIFFRACTION2{ B|* }B-5 - 316
5X-RAY DIFFRACTION2{ B|* }B401 - 512
6X-RAY DIFFRACTION2{ B|* }B601 - 846

+
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