[English] 日本語
Yorodumi
- PDB-4i8o: Crystal structure of the toxin RnlA from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i8o
TitleCrystal structure of the toxin RnlA from Escherichia coli
ComponentsTOXIN RNLA
KeywordsTOXIN / toxin protein
Function / homology
Function and homology information


toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / protein homodimerization activity / cytoplasm
Similarity search - Function
Bacterial toxin RNase RnlA/LsoA, C-terminal Dmd-binding domain / Bacterial toxin RNase RnlA/LsoA, N repeated domain / Bacterial toxin RNase RnlA/LsoA, N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Bacterial toxin, RNase RnlA/LsoA, N-terminal / Bacterial toxin, RNase RnlA/LsoA, N-terminal repeated domain / Bacterial toxin, RNase RnlA/LsoA, DBD domain / RNase LS, bacterial toxin / RNase LS, bacterial toxin DBD domain / RNase LS, bacterial toxin N-terminal ...Bacterial toxin RNase RnlA/LsoA, C-terminal Dmd-binding domain / Bacterial toxin RNase RnlA/LsoA, N repeated domain / Bacterial toxin RNase RnlA/LsoA, N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Bacterial toxin, RNase RnlA/LsoA, N-terminal / Bacterial toxin, RNase RnlA/LsoA, N-terminal repeated domain / Bacterial toxin, RNase RnlA/LsoA, DBD domain / RNase LS, bacterial toxin / RNase LS, bacterial toxin DBD domain / RNase LS, bacterial toxin N-terminal / TATA-Binding Protein / Double Stranded RNA Binding Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase, Ruva Protein; domain 3 / Helix non-globular / Special / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
mRNA endoribonuclease toxin LS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.104 Å
AuthorsWei, Y. / Gao, Z.Q. / Zhang, H. / Dong, Y.H.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Structure-function studies of Escherichia coli RnlA reveal a novel toxin structure involved in bacteriophage resistance.
Authors: Wei, Y. / Gao, Z.Q. / Otsuka, Y. / Naka, K. / Yonesaki, T. / Zhang, H. / Dong, Y.H.
History
DepositionDec 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Dec 3, 2014Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TOXIN RNLA
B: TOXIN RNLA


Theoretical massNumber of molelcules
Total (without water)81,4142
Polymers81,4142
Non-polymers00
Water6,233346
1
A: TOXIN RNLA


Theoretical massNumber of molelcules
Total (without water)40,7071
Polymers40,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TOXIN RNLA


Theoretical massNumber of molelcules
Total (without water)40,7071
Polymers40,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: TOXIN RNLA

B: TOXIN RNLA


Theoretical massNumber of molelcules
Total (without water)81,4142
Polymers81,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1820 Å2
ΔGint-16 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.207, 64.321, 82.623
Angle α, β, γ (deg.)69.24, 79.53, 75.03
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein TOXIN RNLA / toxin protein


Mass: 40706.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: yfjN, b2630, JW2611 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21((DE3) / References: UniProt: P52129
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 2.0 M ammonium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 59960 / Num. obs: 118145 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 26.85
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.85 / Num. unique all: 2927 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
MAR345data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.104→36.504 Å / SU ML: 0.25 / σ(F): 1.96 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 3056 5.1 %RANDOM
Rwork0.1958 ---
all0.1975 59953 --
obs0.1958 59960 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.086 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.5261 Å2-0.5759 Å2-4.4621 Å2
2---6.8206 Å2-0.561 Å2
3----3.7055 Å2
Refinement stepCycle: LAST / Resolution: 2.104→36.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5408 0 0 346 5754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095526
X-RAY DIFFRACTIONf_angle_d1.217499
X-RAY DIFFRACTIONf_dihedral_angle_d13.8372031
X-RAY DIFFRACTIONf_chiral_restr0.08864
X-RAY DIFFRACTIONf_plane_restr0.005963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1042-2.12820.29271580.26463198X-RAY DIFFRACTION81
2.1282-2.15320.26381810.26893623X-RAY DIFFRACTION95
2.1532-2.17940.28961970.26493888X-RAY DIFFRACTION97
2.1794-2.2070.3172040.25963612X-RAY DIFFRACTION95
2.207-2.23610.26482000.2383737X-RAY DIFFRACTION96
2.2361-2.26670.27431960.22863691X-RAY DIFFRACTION96
2.2667-2.29910.2782060.22983811X-RAY DIFFRACTION95
2.2991-2.33340.272020.22713623X-RAY DIFFRACTION97
2.3334-2.36980.28592200.2233787X-RAY DIFFRACTION96
2.3698-2.40870.27272320.23073756X-RAY DIFFRACTION97
2.4087-2.45020.29141700.22593727X-RAY DIFFRACTION97
2.4502-2.49480.29842020.23623819X-RAY DIFFRACTION96
2.4948-2.54270.2571870.21833736X-RAY DIFFRACTION97
2.5427-2.59460.25782200.21553776X-RAY DIFFRACTION96
2.5946-2.6510.25561860.20843731X-RAY DIFFRACTION97
2.651-2.71270.20891780.21773786X-RAY DIFFRACTION96
2.7127-2.78050.29931910.22973713X-RAY DIFFRACTION96
2.7805-2.85560.31541960.22973832X-RAY DIFFRACTION97
2.8556-2.93960.23182140.22433717X-RAY DIFFRACTION96
2.9396-3.03450.25712240.21793767X-RAY DIFFRACTION97
3.0345-3.14290.25152190.21253703X-RAY DIFFRACTION97
3.1429-3.26860.25611780.19873758X-RAY DIFFRACTION96
3.2686-3.41730.231820.18963784X-RAY DIFFRACTION96
3.4173-3.59730.23012120.18793719X-RAY DIFFRACTION96
3.5973-3.82240.20882370.17913672X-RAY DIFFRACTION95
3.8224-4.11720.20112070.16593812X-RAY DIFFRACTION99
4.1172-4.53090.16682190.14793811X-RAY DIFFRACTION99
4.5309-5.18490.2022120.14963850X-RAY DIFFRACTION99
5.1849-6.52630.231870.19833844X-RAY DIFFRACTION99
6.5263-36.50990.15842040.16973841X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 72.3628 Å / Origin y: 70.824 Å / Origin z: 33.551 Å
111213212223313233
T0.2011 Å20.01 Å2-0.001 Å2-0.213 Å20.0044 Å2--0.197 Å2
L0.0705 °20.0651 °20.0473 °2-0.2806 °20.1286 °2--0.1255 °2
S-0.0083 Å °0.0137 Å °0.0018 Å °0.0861 Å °0.01 Å °0.0317 Å °0.0448 Å °0.0869 Å °-0 Å °
Refinement TLS groupSelection details: all

+
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