[English] 日本語
Yorodumi
- PDB-5cr2: E. coli MazF in complex with single strand DNA substrate analog -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cr2
TitleE. coli MazF in complex with single strand DNA substrate analog
Components
  • Endoribonuclease MazF
  • ssDNA substrate analog
KeywordsHYDROLASE / Toxin-Antitoxin / mRNA interferase / ribonuclease / persistence / bacterial stress response
Function / homology
Function and homology information


toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of programmed cell death / regulation of growth / mRNA catabolic process / RNA endonuclease activity / molecular function activator activity ...toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of programmed cell death / regulation of growth / mRNA catabolic process / RNA endonuclease activity / molecular function activator activity / negative regulation of cell growth / regulation of translation / defense response to virus / protein-containing complex binding / regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / DNA binding / RNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
DNA/RNA hybrid / Endoribonuclease toxin MazF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZorzini, V. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO) Belgium
Biostruct-X Belgium
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Substrate Recognition and Activity Regulation of the Escherichia coli mRNA Endonuclease MazF.
Authors: Zorzini, V. / Mernik, A. / Lah, J. / Sterckx, Y.G. / De Jonge, N. / Garcia-Pino, A. / De Greve, H. / Versees, W. / Loris, R.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoribonuclease MazF
B: Endoribonuclease MazF
C: Endoribonuclease MazF
D: ssDNA substrate analog
E: ssDNA substrate analog
F: ssDNA substrate analog


Theoretical massNumber of molelcules
Total (without water)45,0556
Polymers45,0556
Non-polymers00
Water55831
1
A: Endoribonuclease MazF
B: Endoribonuclease MazF
D: ssDNA substrate analog
E: ssDNA substrate analog


Theoretical massNumber of molelcules
Total (without water)30,0374
Polymers30,0374
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Endoribonuclease MazF
F: ssDNA substrate analog

C: Endoribonuclease MazF
F: ssDNA substrate analog


Theoretical massNumber of molelcules
Total (without water)30,0374
Polymers30,0374
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557x-y,-y,-z+8/31
Unit cell
Length a, b, c (Å)113.960, 113.960, 47.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

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


Mass: 12940.904 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: mazF, chpA, chpAK, b2782, JW2753 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AE70, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: DNA/RNA hybrid ssDNA substrate analog


Mass: 2077.385 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage MS2 (virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.17 M Sodium acetate trihydrate, 0.085 M Tris hydrocloride pH 8.5, 25.5% w/v PEG4000, 15% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→42.801 Å / Num. obs: 7461 / % possible obs: 99.4 % / Redundancy: 8.95 % / Rsym value: 0.224 / Net I/σ(I): 8.96
Reflection shellResolution: 2.9→3.17 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 2.25 / Rsym value: 0.778 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDX

4mdx


Resolution: 2.9→42.808 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.87 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2901 391 5.24 %
Rwork0.2232 --
obs0.234 7461 92.25 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.262 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.9839 Å20 Å2-0 Å2
2--3.9839 Å20 Å2
3----12.9347 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 152 0 32 2654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032687
X-RAY DIFFRACTIONf_angle_d0.733676
X-RAY DIFFRACTIONf_dihedral_angle_d14.912991
X-RAY DIFFRACTIONf_chiral_restr0.049420
X-RAY DIFFRACTIONf_plane_restr0.003448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9046-3.32470.33781240.24882340X-RAY DIFFRACTION88
3.3247-4.18830.29621230.22842339X-RAY DIFFRACTION88
4.1883-42.81270.2661260.22422390X-RAY DIFFRACTION87
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)
10.72280.0210.16490.62640.43290.66470.092-0.1443-0.07620.0962-0.01380.0033-0.0239-0.1073-0.02020.1549-0.0372-0.01690.2652-0.01460.0141157.066421.273161.2651
20.84870.3179-0.56481.936-0.08181.3336-0.02040.0295-0.089-0.00220.02830.09560.11480.0561-0.03360.14850.0005-0.02210.1835-0.00560.0436156.470521.804741.7447
31.34780.2305-0.15221.3976-0.16631.4041-0.08040.2326-0.0963-0.18-0.0433-0.09230.0612-0.03850.03310.0736-0.00180.00030.12050.05440.0144131.9342-0.267153.7438
48.29785.02645.91638.7544-0.57687.25-0.03490.52-0.0076-0.505-0.0284-0.49830.05180.7233-0.46070.26360.0278-0.04520.2286-0.05550.3711160.61186.328459.0794
54.70524.2773-4.75138.6737-5.45345.0667-0.56931.5606-0.3598-0.6391-0.17750.1914-0.5104-0.23910.94370.72160.12990.19050.99110.01530.5672145.541722.108734.9737
63.684-3.79632.05325.4698-0.6452.533-0.0403-0.1361-0.0869-0.1276-0.1306-0.12190.6810.89550.08781.1235-0.10560.42330.7856-0.070.6251140.7763-8.101447.4153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain 'A'
2X-RAY DIFFRACTION2Chain 'B'
3X-RAY DIFFRACTION3Chain 'C'
4X-RAY DIFFRACTION4Chain 'D'
5X-RAY DIFFRACTION5Chain 'E'
6X-RAY DIFFRACTION6Chain 'F'

+
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