[English] 日本語
Yorodumi
- PDB-3tnd: Crystal structure of Shigella flexneri VapBC toxin-antitoxin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tnd
TitleCrystal structure of Shigella flexneri VapBC toxin-antitoxin complex
Components
  • Antitoxin VapB
  • tRNA(fMet)-specific endonuclease VapC
KeywordsTRANSLATION / TOXIN / PIN domain / SpoVT/AbrB-like domain / Ribonuclease / DNA-binding
Function / homology
Function and homology information


RNA nuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding
Similarity search - Function
Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / 5'-nuclease / PIN domain ...Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Ribbon / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
tRNA(fMet)-specific endonuclease VapC / Antitoxin VapB
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsDienemann, C. / Boggild, A. / Winther, K.S. / Gerdes, K. / Brodersen, D.E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of the VapBC Toxin-Antitoxin Complex from Shigella flexneri Reveals a Hetero-Octameric DNA-Binding Assembly.
Authors: Dienemann, C. / Boggild, A. / Winther, K.S. / Gerdes, K. / Brodersen, D.E.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: tRNA(fMet)-specific endonuclease VapC
B: Antitoxin VapB
C: tRNA(fMet)-specific endonuclease VapC
D: Antitoxin VapB
E: tRNA(fMet)-specific endonuclease VapC
F: Antitoxin VapB
G: tRNA(fMet)-specific endonuclease VapC
H: Antitoxin VapB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,06521
Polymers96,9628
Non-polymers1,10313
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26700 Å2
ΔGint-242 kcal/mol
Surface area34700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.403, 91.403, 549.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11H-95-

HOH

-
Components

#1: Protein
tRNA(fMet)-specific endonuclease VapC / RNase VapC / Toxin VapC


Mass: 14836.075 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2a / Gene: CP0245, mvpA, stborf2, vapC / Plasmid: pKW812HB / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3)
References: UniProt: O06662, Hydrolases; Acting on ester bonds
#2: Protein
Antitoxin VapB


Mass: 9404.476 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2a / Gene: CP0246, mvpT, vapB / Plasmid: pKW812HB / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: O06663
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.41 Å3/Da / Density % sol: 63.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-tris, 1M ammonium sulphate, 0.5% (v/v) PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.94645
SYNCHROTRONMAX II I911-221.04002
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDApr 15, 2011
MAR CCD 165 mm2CCDMay 20, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Silicon (111) channel-cutSINGLE WAVELENGTHMx-ray1
2Bent Si (111) crystal, horizontally focusingSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
21.040021
ReflectionResolution: 2.6→40 Å / Num. all: 43852 / Num. obs: 43720 / % possible obs: 99.7 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.6-2.661,297.3
2.66-2.741,299.8
2.74-2.821,299.9
2.82-2.91,299.9
2.9-31,2100
3-3.11,2100
3.1-3.221,2100
3.22-3.351,2100
3.35-3.51,2100
3.5-3.671,2100
3.67-3.871,2100
3.67-4.11,2100
4.1-4.391,2100
4.39-4.741,2100
4.74-5.191,2100
5.19-5.81,2100

-
Processing

Software
NameVersionClassification
DNAdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→39.615 Å / SU ML: 0.78 / σ(F): 0 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 1783 4.58 %
Rwork0.1824 --
obs0.1849 38932 99.93 %
all-43720 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.559 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.7565 Å2-0 Å2-0 Å2
2--5.7565 Å2-0 Å2
3----11.5131 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6280 0 57 205 6542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056430
X-RAY DIFFRACTIONf_angle_d0.8388691
X-RAY DIFFRACTIONf_dihedral_angle_d15.4392401
X-RAY DIFFRACTIONf_chiral_restr0.056970
X-RAY DIFFRACTIONf_plane_restr0.0031131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7730.39641350.28972793X-RAY DIFFRACTION100
2.773-2.85460.38061340.26852773X-RAY DIFFRACTION100
2.8546-2.94670.29121330.22292781X-RAY DIFFRACTION100
2.9467-3.0520.27851360.20812798X-RAY DIFFRACTION100
3.052-3.17410.26731330.19912768X-RAY DIFFRACTION100
3.1741-3.31850.25211340.19812804X-RAY DIFFRACTION100
3.3185-3.49340.26251360.19192814X-RAY DIFFRACTION100
3.4934-3.71210.23561350.17472824X-RAY DIFFRACTION100
3.7121-3.99850.22451370.16222860X-RAY DIFFRACTION100
3.9985-4.40040.19841380.13852881X-RAY DIFFRACTION100
4.4004-5.0360.20621380.14172897X-RAY DIFFRACTION100
5.036-6.34070.20121410.18512966X-RAY DIFFRACTION100
6.3407-39.61930.22911530.19593190X-RAY DIFFRACTION100

+
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