[English] 日本語
Yorodumi
- PDB-2a6s: Crystal structure of YoeB under isopropanol condition -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a6s
TitleCrystal structure of YoeB under isopropanol condition
ComponentsToxin yoeB
KeywordsTOXIN / YoeB / YefM / antitoxin / addiction modules / RNase / inhibitor
Function / homology
Function and homology information


global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters / response to heat ...global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters / response to heat / endonuclease activity / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding
Similarity search - Function
Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Toxin YoeB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsKamada, K. / Hanaoka, F.
CitationJournal: Mol.Cell / Year: 2005
Title: Conformational Change in the Catalytic Site of the Ribonuclease YoeB Toxin by YefM Antitoxin
Authors: Kamada, K. / Hanaoka, F.
History
DepositionJul 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toxin yoeB
B: Toxin yoeB
C: Toxin yoeB
D: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,29510
Polymers40,9354
Non-polymers3616
Water5,657314
1
A: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2942
Polymers10,2341
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4144
Polymers10,2341
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2942
Polymers10,2341
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2942
Polymers10,2341
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.974, 60.989, 98.560
Angle α, β, γ (deg.)90.00, 98.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Toxin yoeB


Mass: 10233.658 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yoeB / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P69348
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, CH3COONH4, isopropanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.2K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2004 / Details: Collimating and Focusing mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→48.8 Å / Num. all: 33197 / Num. obs: 33168 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 14.8 Å2 / Χ2: 1.339 / Net I/σ(I): 42.01
Reflection shellResolution: 1.77→1.83 Å / % possible obs: 97.5 % / Redundancy: 6.8 % / Num. measured obs: 3248 / Num. unique all: 3248 / Χ2: 0.954 / % possible all: 97.5

-
Phasing

Phasing MRCor.coef. Fo:Fc: 0.489 / Packing: 0.624
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral99.2 0

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: extracted from YoeB structure from 2A6Q

2a6q


Resolution: 1.77→19.96 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1649 5 %random
Rwork0.195 ---
all0.197 33154 --
obs0.196 33036 99.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 55.633 Å2 / ksol: 0.446303 e/Å3
Displacement parametersBiso max: 55.56 Å2 / Biso mean: 17.15 Å2 / Biso min: 4.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å22.16 Å2
2--0.14 Å20 Å2
3---0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å-0.06 Å
Luzzati d res high-1.77
Refinement stepCycle: LAST / Resolution: 1.77→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 0 338 3204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.4171.5
X-RAY DIFFRACTIONc_mcangle_it2.2932
X-RAY DIFFRACTIONc_scbond_it2.2252
X-RAY DIFFRACTIONc_scangle_it3.4032.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.77-1.850.221894.70.19438620.0164123405198.3
1.85-1.950.2442105.10.19139270.0174166413799.3
1.95-2.070.2351884.60.18339380.0174154412699.3
2.07-2.230.191974.80.17739320.0144148412999.5
2.23-2.450.2212225.40.19138780.0154117410099.6
2.45-2.810.2331994.80.20739460.0164154414599.8
2.81-3.540.2332115.10.19739460.0164166415799.8
3.54-19.960.222335.60.20139580.0144227419199.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ioh_xplor_par.txtIOH_XPLOR_top.TXT

+
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