[English] 日本語
Yorodumi
- PDB-4me7: Crystal structure of Bacillus subtilis toxin MazF in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4me7
TitleCrystal structure of Bacillus subtilis toxin MazF in complex with cognate antitoxin MazE
Components
  • Antitoxin EndoAI
  • mRNA interferase EndoA
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Toxin-antitoxin system / MazE-MazF / Stress response / mRNA clevage / MazE / Antitoxin / MazF / mRNA interferase / EndoA / YdcE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


rRNA catabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA catabolic process / RNA endonuclease activity / regulation of DNA-templated transcription / DNA binding / RNA binding / identical protein binding
Similarity search - Function
SH3 type barrels. - #110 / Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix ...SH3 type barrels. - #110 / Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / SH3 type barrels. / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Antitoxin EndoAI / Endoribonuclease EndoA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.918 Å
AuthorsSimanshu, D.K. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2013
Title: Structural Basis of mRNA Recognition and Cleavage by Toxin MazF and Its Regulation by Antitoxin MazE in Bacillus subtilis.
Authors: Simanshu, D.K. / Yamaguchi, Y. / Park, J.H. / Inouye, M. / Patel, D.J.
History
DepositionAug 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 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 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mRNA interferase EndoA
B: mRNA interferase EndoA
C: mRNA interferase EndoA
D: mRNA interferase EndoA
E: Antitoxin EndoAI
F: Antitoxin EndoAI


Theoretical massNumber of molelcules
Total (without water)74,4016
Polymers74,4016
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint-75 kcal/mol
Surface area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.503, 91.618, 104.334
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and (resseq 1:16 or resseq 24:113 )
21chain D and (resseq 1:16 or resseq 24:113 )
31chain C and (resseq 1:16 or resseq 24:113 )
12chain E and (resseq 7:83 )
22chain F and (resseq 7:83 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'B' and (resseq 1:16 or resseq 24:113 )B1 - 16
121chain 'B' and (resseq 1:16 or resseq 24:113 )B24 - 113
211chain 'D' and (resseq 1:16 or resseq 24:113 )D1 - 16
221chain 'D' and (resseq 1:16 or resseq 24:113 )D24 - 113
311chain 'C' and (resseq 1:16 or resseq 24:113 )C1 - 16
321chain 'C' and (resseq 1:16 or resseq 24:113 )C24 - 113
112chain 'E' and (resseq 7:83 )E7 - 83
212chain 'F' and (resseq 7:83 )F7 - 83

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.985198, -0.116141, 0.126076), (-0.135202, -0.074343, 0.988025), (-0.105378, -0.990447, -0.088945)-47.304298, 41.194099, 2.95518
2given(-0.999861, -0.002911, -0.016397), (0.000494, -0.989356, 0.145511), (-0.016646, 0.145483, 0.989221)-40.903702, 45.1427, -3.10509
3given(-0.999882, -0.006747, -0.013781), (0.004286, -0.985201, 0.171352), (-0.014733, 0.171273, 0.985113)-40.610401, 45.611, -4.18004

-
Components

#1: Protein
mRNA interferase EndoA / Endoribonuclease EndoA / Toxin EndoA / mRNA interferase MazF-bs / MazF-bs


Mass: 13134.627 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU04660, mazF, ndoA, ydcE / Plasmid: pRSF-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P96622, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin EndoAI / Antitoxin MazE-bs / MazE-bs / EndoA inhibitor


Mass: 10931.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MazE and MazF proteins were co-expressed in E. coli.
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU04650, mazE, ndoAI / Plasmid: pRSF-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P96621
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium chloride, 0.1 M Bis-Tris pH 6.5 and 3% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 5.6 % / Number: 95544 / Rmerge(I) obs: 0.102 / Χ2: 3.15 / D res high: 2.92 Å / D res low: 30 Å / Num. obs: 17173 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.273099.210.07911.7775
4.996.2799.910.1046.1225.5
4.364.9999.910.0874.0815.6
3.964.3610010.0982.9485.7
3.683.9610010.1312.0695.8
3.463.6810010.1621.4515.8
3.293.4610010.2241.135.9
3.153.2999.910.3430.8685.9
3.023.1599.310.4740.7135.5
2.923.0296.610.6440.6495
ReflectionResolution: 2.918→45.33 Å / Num. obs: 17226 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 90.67 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 31.6
Reflection shellResolution: 2.918→3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1.85 / Num. unique all: 1648 / % possible all: 97.2

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 4MDX

4mdx


Resolution: 2.918→45.33 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6855 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2989 1714 10 %Random
Rwork0.253 ---
obs0.2574 17139 97.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.84 Å2 / Biso mean: 60.5104 Å2 / Biso min: 21.34 Å2
Refinement stepCycle: LAST / Resolution: 2.918→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4609 0 0 30 4639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074653
X-RAY DIFFRACTIONf_angle_d1.0856266
X-RAY DIFFRACTIONf_chiral_restr0.067751
X-RAY DIFFRACTIONf_plane_restr0.003806
X-RAY DIFFRACTIONf_dihedral_angle_d14.6761796
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B798X-RAY DIFFRACTIONTORSIONAL0.076
12D798X-RAY DIFFRACTIONTORSIONAL0.076
13C838X-RAY DIFFRACTIONTORSIONAL0.065
21E614X-RAY DIFFRACTIONTORSIONAL0.063
22F614X-RAY DIFFRACTIONTORSIONAL0.063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9179-3.00370.44411090.3565987109677
3.0037-3.10070.37291410.35581263140498
3.1007-3.21150.38761440.324912851429100
3.2115-3.340.36051430.29712911434100
3.34-3.4920.32511450.277113021447100
3.492-3.6760.29321450.268213071452100
3.676-3.90620.34481440.257912981442100
3.9062-4.20760.29311460.240213141460100
4.2076-4.63060.27221450.205813101455100
4.6306-5.29980.26771480.221513361484100
5.2998-6.67380.30571510.267413491500100
6.6738-45.33870.27191530.24831383153698
Refinement TLS params.Method: refined / Origin x: -20.2013 Å / Origin y: 21.1067 Å / Origin z: -24.0215 Å
111213212223313233
T0.3477 Å20.0916 Å2-0.0047 Å2-0.314 Å20.0566 Å2--0.2255 Å2
L3.3098 °21.0549 °2-0.2562 °2-0.9715 °2-0.2527 °2--0.5537 °2
S0.0271 Å °0.6349 Å °0.0141 Å °-0.0248 Å °-0.0296 Å °-0.0319 Å °0.0874 Å °0.0156 Å °0.0411 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 114
2X-RAY DIFFRACTION1allB1 - 114
3X-RAY DIFFRACTION1allC1 - 114
4X-RAY DIFFRACTION1allD1 - 114
5X-RAY DIFFRACTION1allE6 - 83
6X-RAY DIFFRACTION1allF7 - 85
7X-RAY DIFFRACTION1allC - A1 - 205

+
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://pdbjlvh1.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