[English] 日本語
Yorodumi
- PDB-4fxh: Crystal structure of the isolated E. coli RelE toxin, P212121 form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fxh
TitleCrystal structure of the isolated E. coli RelE toxin, P212121 form
ComponentsmRNA interferase RelE
KeywordsTOXIN / toxin/antitoxin system / nuclease / translational control / stress response / RelB / Ribosome / B-ME on Cys50
Function / homology
Function and homology information


toxin sequestering activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / mRNA catabolic process / RNA endonuclease activity / cellular response to amino acid starvation / protein-DNA complex / ribosome binding ...toxin sequestering activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / mRNA catabolic process / RNA endonuclease activity / cellular response to amino acid starvation / protein-DNA complex / ribosome binding / endonuclease activity / Hydrolases; Acting on ester bonds / transcription cis-regulatory region binding / negative regulation of translation / rRNA binding / response to antibiotic / regulation of DNA-templated transcription
Similarity search - Function
ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
mRNA interferase toxin RelE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBrodersen, D.E. / Boggild, A. / Sofos, N.
CitationJournal: Structure / Year: 2012
Title: The crystal structure of the intact E. coli RelBE toxin-antitoxin complex provides the structural basis for conditional cooperativity.
Authors: Boggild, A. / Sofos, N. / Andersen, K.R. / Feddersen, A. / Easter, A.D. / Passmore, L.A. / Brodersen, D.E.
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mRNA interferase RelE
B: mRNA interferase RelE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5693
Polymers22,4732
Non-polymers961
Water3,495194
1
A: mRNA interferase RelE


Theoretical massNumber of molelcules
Total (without water)11,2361
Polymers11,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA interferase RelE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3322
Polymers11,2361
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-7 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.631, 61.443, 63.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein mRNA interferase RelE / Endoribonuclease RelE / Toxin RelE


Mass: 11236.251 Da / Num. of mol.: 2 / Fragment: RelE / Mutation: R81A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1563, JW1555, relE / Plasmid: pSC2524HE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0C077, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 0.2 M ammonium sulphate, 30% PEG 5000 MME, pH 6.5, vapor diffusion, sitting drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.91838 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91838 Å / Relative weight: 1
ReflectionResolution: 2.3→44.291 Å / Num. all: 8223 / Num. obs: 8223 / % possible obs: 96.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 40.7 Å2 / Rsym value: 0.049 / Net I/σ(I): 18.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.364.10.1515.124846010.15198
2.36-2.424.10.1345.724435900.13497.8
2.42-2.494.10.1166.623915790.11698.2
2.49-2.574.10.1037.323475750.10398.1
2.57-2.664.20.0928.321995210.09296.4
2.66-2.754.10.0819.521135160.08197.3
2.75-2.854.20.06910.421225060.06997.4
2.85-2.974.10.06111.619904850.06197.1
2.97-3.14.20.04913.219344650.04996.4
3.1-3.254.20.04714.318494440.04797.6
3.25-3.434.20.04114.617694230.04196.4
3.43-3.644.10.04513.716624020.04596.3
3.64-3.894.10.0491315663790.04996.3
3.89-4.24.20.05111.614563500.05196.9
4.2-4.64.10.0511.613613300.0596.3
4.6-5.144.10.04214.712232980.04295.5
5.14-5.944.10.03815.110662630.03895.6
5.94-7.274.10.03513.79072200.03595
7.27-10.2940.02817.56891730.02892.4
10.29-44.2913.70.02819.13761030.02887.6

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KHA

3kha
PDB Unreleased entry


Resolution: 2.4→37.669 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.7941 / SU ML: 0.39 / σ(F): 1.39 / Phase error: 26.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 350 4.85 %Random
Rwork0.2357 ---
obs0.238 7220 95.26 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.36 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 119.39 Å2 / Biso mean: 47.4198 Å2 / Biso min: 5.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.5881 Å20 Å2-0 Å2
2--0.6751 Å20 Å2
3----2.2632 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 5 194 1712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041551
X-RAY DIFFRACTIONf_angle_d0.8272077
X-RAY DIFFRACTIONf_chiral_restr0.057232
X-RAY DIFFRACTIONf_plane_restr0.004257
X-RAY DIFFRACTIONf_dihedral_angle_d20.435629
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.74720.3341190.286422612380226197
2.7472-3.46080.33941210.243922882409228896
3.4608-37.67330.23661100.215923212431232193
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)
16.1785-0.1694-1.01644.7509-1.1972.0919-0.17630.64690.0696-0.43520.1090.2948-0.0759-0.16880.00490.40510.0643-0.15910.1905-0.03080.2756-0.2722-15.2763-15.8531
24.9195-2.84663.80733.7407-2.48987.81050.2948-0.003-1.2397-0.20411.17681.39191.4535-0.7995-1.28480.5613-0.13580.09160.62860.16270.8647-3.11-24.8727-10.5237
36.4759-0.27290.89526.350.82156.2504-0.2854-0.54540.18940.51430.3856-0.60090.00930.239-0.09050.18980.08570.01870.3132-0.0370.21467.5281-14.1397-7.1067
44.2331-1.35411.15057.1769-0.10264.59580.98360.2072-0.5695-0.0171-0.0026-0.86870.50290.0989-0.74630.38070.34380.21271.0525-0.43320.957110.9152-31.6435-16.5502
52.2074-1.20381.194.84890.28022.1137-0.20080.29660.2268-0.27680.38240.1547-0.10440.61950.02840.2794-0.0274-0.02770.3108-0.03510.43019.5401-43.1749-18.7901
63.7981-1.003-1.76981.9865-2.08024.57930.82771.0512-0.8271-0.24410.7939-0.46770.37440.3353-0.6883-0.84670.737-0.13880.6087-0.7771.754523.5555-47.7149-13.1021
72.03316.43035.32998.73817.60862.0281-0.81990.89790.7391-1.55820.35090.5066-0.82751.86960.40480.7389-0.06340.12630.4589-0.05770.391624.7341-35.453-18.1848
85.52472.35382.85942.7422-0.0882.4442-0.72770.67780.1041-0.86190.43-0.78980.04210.738-0.05371.00380.39230.16991.1928-0.25660.698332.4571-30.5592-10.9531
97.46451.1032-0.54667.68822.24433.73550.4118-0.1224-1.08981.3820.7203-1.9784-0.27461.4865-0.9640.7023-0.0577-0.33750.5499-0.07970.492428.8831-39.0321-4.347
106.32480.7189-0.84592.046-1.03760.87821.3321-1.7769-1.47340.957-0.03020.02870.2678-0.5525-0.90390.896-0.0522-0.2180.62740.10130.62918.6732-46.889-1.1686
119.68221.7392-3.88592.15730.17925.88080.0518-1.35780.23640.3915-0.81711.4313-0.7841-2.96631.23130.70860.10190.03240.7084-0.18880.46269.5187-41.2763-7.2572
127.43157.06990.37062.0139-2.98263.48411.3328-0.89840.78131.9615-0.22891.2666-0.1608-0.4498-0.73310.4738-0.12490.09340.5726-0.16450.309221.5072-31.8588-1.7482
132.4686.08520.52758.8456-0.7755.73930.3721-0.0924-0.7712-0.4614-0.3975-0.55340.6811-0.61870.06260.38420.0455-0.10180.4173-0.0410.346717.3374-43.7751-10.1267
144.963-1.12640.46257.93772.60364.88320.03130.04670.3292-0.69320.1842-0.766-0.1572-0.3936-0.05450.25830.0803-0.02350.3083-0.0730.194319.5365-35.5908-12.1892
156.65615.6108-0.36032.036-6.28456.9735-0.00640.7685-0.4186-0.1454-0.6416-1.19250.15780.30010.50340.36740.17110.00290.65110.00210.250312.7825-17.6509-18.1793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:15)A2 - 15
2X-RAY DIFFRACTION2chain 'A' and (resseq 16:33)A16 - 33
3X-RAY DIFFRACTION3chain 'A' and (resseq 34:78)A34 - 78
4X-RAY DIFFRACTION4chain 'A' and (resseq 79:83)A79 - 83
5X-RAY DIFFRACTION5chain 'A' and (resseq 84:95)A84 - 95
6X-RAY DIFFRACTION6chain 'B' and (resseq 2:8)B2 - 8
7X-RAY DIFFRACTION7chain 'B' and (resseq 9:15)B9 - 15
8X-RAY DIFFRACTION8chain 'B' and (resseq 16:21)B16 - 21
9X-RAY DIFFRACTION9chain 'B' and (resseq 22:33)B22 - 33
10X-RAY DIFFRACTION10chain 'B' and (resseq 34:42)B34 - 42
11X-RAY DIFFRACTION11chain 'B' and (resseq 43:51)B43 - 51
12X-RAY DIFFRACTION12chain 'B' and (resseq 52:59)B52 - 59
13X-RAY DIFFRACTION13chain 'B' and (resseq 60:70)B60 - 70
14X-RAY DIFFRACTION14chain 'B' and (resseq 71:84)B71 - 84
15X-RAY DIFFRACTION15chain 'B' and (resseq 85:95)B85 - 95

+
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