[English] 日本語
Yorodumi
- PDB-2xdd: A processed non-coding RNA regulates a bacterial antiviral system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xdd
TitleA processed non-coding RNA regulates a bacterial antiviral system
Components
  • TOXI
  • TOXN
KeywordsTOXIN/RNA / TOXIN-RNA COMPLEX / ABORTIVE INFECTION / PHAGE / TOXIN
Function / homology
Function and homology information


plasmid maintenance / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription / RNA binding / identical protein binding
Similarity search - Function
ToxN/AbiQ toxin / : / Toxin ToxN, type III toxin-antitoxin system / Thiol Ester Dehydrase; Chain A - #130 / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Endoribonuclease ToxN
Similarity search - Component
Biological speciesPECTOBACTERIUM ATROSEPTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsBlower, T.R. / Pei, X.Y. / Short, F.L. / Fineran, P.C. / Humphreys, D.P. / Luisi, B.F. / Salmond, G.P.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The Phage Abortive Infection System, Toxin, Functions as a Protein-RNA Toxin-Antitoxin Pair.
Authors: Fineran, P.C. / Blower, T.R. / Foulds, I.J. / Humphreys, D.P. / Lilley, K.S. / Salmond, G.P.C.
History
DepositionApr 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: TOXN
B: TOXN
E: TOXN
F: TOXI
G: TOXI
H: TOXI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,39518
Polymers94,6106
Non-polymers78512
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15870 Å2
ΔGint-410.6 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.850, 118.130, 41.900
Angle α, β, γ (deg.)90.00, 92.78, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:162)
211CHAIN B AND (RESSEQ 1:162)
311CHAIN E AND (RESSEQ 1:162)

-
Components

#1: Protein TOXN


Mass: 19961.014 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PECTOBACTERIUM ATROSEPTICUM (bacteria) / Strain: SCRI 1039 / Description: ENVIRONMENTAL ISOLATED FROM SCOTLAND, U.K / Plasmid: PTYB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: B8X8Z0, EC: 3.1.27.3
#2: RNA chain TOXI


Mass: 11575.790 Da / Num. of mol.: 3 / Fragment: RESIDUES 1775-1814
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PECTOBACTERIUM ATROSEPTICUM (bacteria) / Description: ENVIRONMENTAL ISOLATED FROM SCOTLAND, U.K / Plasmid: PACYC184 / Production host: ESCHERICHIA COLI (E. coli) / References: GenBank: FJ176937
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTOXI IS A NONCODING ANTITOXIN RNA TO TOXN TOXIC PROTEIN TOXI CORRESPONDS TO PECA1039 PLASMID ...TOXI IS A NONCODING ANTITOXIN RNA TO TOXN TOXIC PROTEIN TOXI CORRESPONDS TO PECA1039 PLASMID NUCLEOTIDES 1706-1957.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.5 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.01M ZNSO4, 0.1M MES PH6.5, 25% PEG MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9801
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 9, 2009 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.2→35 Å / Num. obs: 14694 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Biso Wilson estimate: 62.34 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.1
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.2→34.9 Å / SU ML: 0.47 / σ(F): 1.39 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 2879 10 %
Rwork0.188 --
obs0.194 28776 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.73 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0183 Å20 Å2-2.647 Å2
2--3.4314 Å20 Å2
3----3.4131 Å2
Refinement stepCycle: LAST / Resolution: 3.2→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 2292 12 56 6308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016594
X-RAY DIFFRACTIONf_angle_d2.669411
X-RAY DIFFRACTIONf_dihedral_angle_d22.3222892
X-RAY DIFFRACTIONf_chiral_restr0.0851128
X-RAY DIFFRACTIONf_plane_restr0.009801
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1316X-RAY DIFFRACTIONPOSITIONAL
12B1316X-RAY DIFFRACTIONPOSITIONAL0.05
13E1316X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.25250.36571320.28361188X-RAY DIFFRACTION100
3.2525-3.30850.28441400.2311190X-RAY DIFFRACTION100
3.3085-3.36860.30581330.22041255X-RAY DIFFRACTION100
3.3686-3.43330.29421270.22971262X-RAY DIFFRACTION100
3.4333-3.50340.28361520.21211241X-RAY DIFFRACTION100
3.5034-3.57950.28841310.21741226X-RAY DIFFRACTION100
3.5795-3.66260.34891450.19661194X-RAY DIFFRACTION100
3.6626-3.75410.2411430.18451262X-RAY DIFFRACTION100
3.7541-3.85550.21891280.18111272X-RAY DIFFRACTION100
3.8555-3.96880.22171400.15361194X-RAY DIFFRACTION100
3.9688-4.09670.19621270.13991258X-RAY DIFFRACTION100
4.0967-4.24290.17931410.13631249X-RAY DIFFRACTION100
4.2429-4.41250.20411430.14791203X-RAY DIFFRACTION100
4.4125-4.61290.18761400.13411254X-RAY DIFFRACTION100
4.6129-4.85550.23281340.14791220X-RAY DIFFRACTION100
4.8555-5.15880.22591330.15221278X-RAY DIFFRACTION100
5.1588-5.55560.22971420.16231192X-RAY DIFFRACTION100
5.5556-6.1120.26391400.1771262X-RAY DIFFRACTION100
6.112-6.99030.25481400.19481242X-RAY DIFFRACTION100
6.9903-8.78370.30671350.19451215X-RAY DIFFRACTION100
8.7837-34.89880.27441330.21521240X-RAY DIFFRACTION99
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)
14.8937-1.80170.66424.5032-0.19713.6332-0.06620.067-0.16680.0449-0.1313-0.23110.43730.05480.16260.09340.02480.04050.0982-0.0469-0.133163.618338.535-6.7206
23.58840.34681.01633.14330.13552.6536-0.0997-0.10010.4515-0.3609-0.07320.10560.06040.25520.17360.08480.0902-0.09540.1045-0.06890.182419.174466.6467-17.2619
32.29880.1293-0.27415.07090.92514.6074-0.41760.2898-0.19990.2919-0.19481.5515-0.065-0.47210.27050.126-0.02210.19190.1646-0.08920.561517.0113.5517-12.0634
46.52613.45462.23692.05760.5429-1.34540.1925-0.0291-0.4091-0.14280.0481-0.2606-0.2920.05770.01050.371-0.13050.03290.4184-0.19020.22142.543820.6154-15.3368
56.6916-4.69580.30821.6884-2.0698-2.1496-0.28660.10850.2939-0.2761-0.07050.3691-0.2548-0.2863-0.19660.32710.105-00.3174-0.03670.056646.055856.7871-16.9951
61.95392.41471.20744.3079-1.6573-1.51810.09540.1851-0.7836-0.7553-0.2964-0.3391-0.0326-0.15750.11560.53170.06940.00860.0372-0.09740.424714.257740.4421-20.9677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN E
4X-RAY DIFFRACTION4CHAIN G
5X-RAY DIFFRACTION5CHAIN H
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://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