[English] 日本語
Yorodumi
- PDB-6gtr: Structure of the AtaT Y144F mutant toxin bound to the C-terminus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gtr
TitleStructure of the AtaT Y144F mutant toxin bound to the C-terminus of the antitoxin AtaR and Acetyl-CoA
Components
  • DUF1778 domain-containing protein
  • N-acetyltransferase
KeywordsTRANSCRIPTION / TA toxin / antitoxin / N-acetyl transferase / ribbon-helix-helix / RHH / bacterial repressor / toxin-antitoxin complex
Function / homology
Function and homology information


toxin sequestering activity / regulation of DNA-templated transcription
Similarity search - Function
Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / Acetyltransferase (GNAT) domain / Ribbon-helix-helix / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / N-acetyltransferase / DUF1778 domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsGarcia-Pino, A. / Jurenas, D.
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Mechanism of regulation and neutralization of the AtaR-AtaT toxin-antitoxin system.
Authors: Jurenas, D. / Van Melderen, L. / Garcia-Pino, A.
History
DepositionJun 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: N-acetyltransferase
B: N-acetyltransferase
C: DUF1778 domain-containing protein
D: DUF1778 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2367
Polymers50,3104
Non-polymers9263
Water59433
1
A: N-acetyltransferase
C: DUF1778 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9894
Polymers25,1552
Non-polymers8342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-37 kcal/mol
Surface area9840 Å2
MethodPISA
2
B: N-acetyltransferase
D: DUF1778 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2473
Polymers25,1552
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-28 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.880, 87.880, 125.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein N-acetyltransferase


Mass: 19900.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BWP17_00640, CVH05_12355
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1V3CQ74
#2: Protein/peptide DUF1778 domain-containing protein / Toxin-antitoxin system / antitoxin component / ribbon-helix-helix fold protein / Ybl13


Mass: 5254.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: J7QA90

-
Non-polymers , 4 types, 36 molecules

#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M citrate, 20%(w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.99→45.54 Å / Num. obs: 11694 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 69.84 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.6
Reflection shellResolution: 2.99→3.11 Å / Rmerge(I) obs: 0.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GTQ

6gtq


Resolution: 2.99→45.54 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.399
RfactorNum. reflection% reflectionSelection details
Rfree0.26 585 5 %RANDOM
Rwork0.193 ---
obs0.196 11694 99.8 %-
Displacement parametersBiso mean: 58.14 Å2
Baniso -1Baniso -2Baniso -3
1--6.8427 Å20 Å20 Å2
2---6.8427 Å20 Å2
3---13.6855 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.99→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 58 34 3107
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013144HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.194272HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1063SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes529HARMONIC5
X-RAY DIFFRACTIONt_it3144HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion22.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3509SEMIHARMONIC4
LS refinement shellResolution: 3→3.28 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3448 136 5 %
Rwork0.2321 2582 -
all0.2374 2718 -
obs--99.2 %
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)
12.4811.70182.33.77223.03554.0306-0.05530.2755-0.0806-0.13440.1958-0.2252-0.14710.4174-0.1405-0.1123-0.14090.0818-0.0204-0.0221-0.1162-17.795635.7569-21.0193
25.06061.1549-3.0053.31910.5433.84290.31-0.52010.29430.0488-0.0674-0.0456-0.31170.3455-0.2425-0.1805-0.1430.0041-0.0618-0.0695-0.1732-32.417939.0314.5999
35.51440.35992.69644.52520.98820.4795-0.1560.29360.1778-0.23890.3636-0.2382-0.04110.002-0.2077-0.0586-0.1610.1198-0.0398-0.0026-0.0407-10.872944.4431-13.9519
42.31670.32783.16894.4463-2.09256.1689-0.07990.1379-0.2014-0.16320.025-0.06650.13790.040.0549-0.1541-0.14930.0106-0.0798-0.0311-0.0244-33.458525.28161.6318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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