[English] 日本語
Yorodumi
- PDB-2xd0: A processed non-coding RNA regulates a bacterial antiviral system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xd0
TitleA processed non-coding RNA regulates a bacterial antiviral system
Components
  • TOXI
  • TOXN
KeywordsTOXIN/RNA / TOXIN-RNA COMPLEX / ABORTIVE INFECTION / PHAGE
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)
Pectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBlower, T.R. / Pei, X.Y. / Short, F.L. / Fineran, P.C. / Humphreys, D.P. / Luisi, B.F. / Salmond, G.P.C.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2011
Title: A processed noncoding RNA regulates an altruistic bacterial antiviral system.
Authors: Blower, T.R. / Pei, X.Y. / Short, F.L. / Fineran, P.C. / Humphreys, D.P. / Luisi, B.F. / Salmond, G.P.
History
DepositionApr 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 30, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Experimental preparation
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / database_PDB_caveat / exptl_crystal_grow / pdbx_validate_chiral
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 2.1Jun 3, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Source and taxonomy
Category: pdbx_database_status / pdbx_entity_src_syn ...pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _pdbx_database_status.status_code_sf / _pdbx_validate_close_contact.auth_asym_id_1 ..._pdbx_database_status.status_code_sf / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.dist / _struct_conf.pdbx_PDB_helix_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TOXN
B: TOXN
E: TOXN
G: TOXI
H: TOXI
I: TOXI
U: TOXI
V: TOXI
W: TOXI
X: TOXN
Y: TOXN
Z: TOXN


Theoretical massNumber of molelcules
Total (without water)187,81412
Polymers187,81412
Non-polymers00
Water3,081171
1
V: TOXI
Y: TOXN


Theoretical massNumber of molelcules
Total (without water)31,3022
Polymers31,3022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-15 kcal/mol
Surface area14130 Å2
MethodPISA
2
A: TOXN
G: TOXI


Theoretical massNumber of molelcules
Total (without water)31,3022
Polymers31,3022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-15.5 kcal/mol
Surface area14190 Å2
MethodPISA
3
B: TOXN
H: TOXI


Theoretical massNumber of molelcules
Total (without water)31,3022
Polymers31,3022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-14.3 kcal/mol
Surface area14200 Å2
MethodPISA
4
E: TOXN
I: TOXI


Theoretical massNumber of molelcules
Total (without water)31,3022
Polymers31,3022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-13.5 kcal/mol
Surface area14200 Å2
MethodPISA
5
W: TOXI
Z: TOXN


Theoretical massNumber of molelcules
Total (without water)31,3022
Polymers31,3022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-11.4 kcal/mol
Surface area14280 Å2
MethodPISA
6
U: TOXI
X: TOXN


Theoretical massNumber of molelcules
Total (without water)31,3022
Polymers31,3022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-10.4 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.139, 119.125, 377.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:161 )
211CHAIN B AND (RESSEQ 1:161 )
311CHAIN E AND (RESSEQ 1:161 )
411CHAIN X AND (RESSEQ 1:161 )
511CHAIN Y AND (RESSEQ 1:161 )
611CHAIN Z AND (RESSEQ 1:161 )

NCS oper:
IDCodeMatrixVector
1given(0.9601, -0.2303, 0.1589), (0.012, -0.5335, -0.8457), (0.2795, 0.8139, -0.5094)-12.68, 68.44, 125.1
2given(-0.9998, -0.02033, 0.005701), (-0.02024, 0.9997, 0.01558), (-0.006016, 0.01547, -0.9999)-7.294, -0.9661, 95.32
3given(0.9863, 0.05864, 0.154), (-0.104, -0.5039, 0.8575), (0.1279, -0.8618, -0.4909)-11.8, -71.59, 121.3
4given(-0.9514, -0.267, -0.1538), (0.01844, -0.5475, 0.8366), (-0.3076, 0.793, 0.5258)-2.597, -11.56, 74.46
5given(-0.9976, -0.05132, -0.04573), (0.06498, -0.4871, -0.8709), (0.02242, -0.8718, 0.4893)-6.181, 11.97, 73.19

-
Components

#1: Protein
TOXN


Mass: 19726.537 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PECTOBACTERIUM ATROSEPTICUM (bacteria) / Strain: SCRI 1039 / Description: ENVIRONMENTAL ISOLATE 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.: 6 / Fragment: BACTERIA ANTITOX, RESIDUES 1775-1810 / Source method: obtained synthetically / Source: (synth.) Pectobacterium atrosepticum (bacteria) / References: GenBank: FJ176937
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRNA DERIVED FROM 252 NUCLEOTIDE TOXI NON-CODING RNA OF PECA1039 PLASMID. RNA BOUND CORRESPONDS TO ...RNA DERIVED FROM 252 NUCLEOTIDE TOXI NON-CODING RNA OF PECA1039 PLASMID. RNA BOUND CORRESPONDS TO NUCLEOTIDES 1775-1810 (WHICH IS 70-104 OF TOXI TRANSCRIPT) AND WHICH HAS UNDERGONE 3' HYDROLYSIS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.6M NACL, 0.1M MES PH6.5, 20% W/V PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 19, 2008 / Details: SINGLE SILICON (111) MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. obs: 35628 / % possible obs: 89.7 % / Observed criterion σ(I): 3 / Redundancy: 6.2 % / Biso Wilson estimate: 50.38 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18
Reflection shellHighest resolution: 3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.4 / % possible all: 66.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6_289)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEM MODEL OF TOXIN COMPLEX FROM SAME STUDY

Resolution: 3→35 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 1734 4.9 %
Rwork0.214 --
obs0.216 35161 89.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.21 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.1438 Å2-0 Å2-0 Å2
2---12.8967 Å20 Å2
3----15.0855 Å2
Refinement stepCycle: LAST / Resolution: 3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7896 4584 0 171 12651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113194
X-RAY DIFFRACTIONf_angle_d1.64218846
X-RAY DIFFRACTIONf_dihedral_angle_d20.3215670
X-RAY DIFFRACTIONf_chiral_restr0.0822220
X-RAY DIFFRACTIONf_plane_restr0.0091608
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1307X-RAY DIFFRACTIONPOSITIONAL
12B1307X-RAY DIFFRACTIONPOSITIONAL0.061
13E1307X-RAY DIFFRACTIONPOSITIONAL0.066
14X1307X-RAY DIFFRACTIONPOSITIONAL0.056
15Y1307X-RAY DIFFRACTIONPOSITIONAL0.062
16Z1307X-RAY DIFFRACTIONPOSITIONAL0.056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.08840.3519930.31641921X-RAY DIFFRACTION63
3.0884-3.1880.3562950.30112099X-RAY DIFFRACTION68
3.188-3.30190.32461210.26992247X-RAY DIFFRACTION73
3.3019-3.4340.2891360.24752293X-RAY DIFFRACTION75
3.434-3.59010.25821450.24092720X-RAY DIFFRACTION88
3.5901-3.77920.25681480.21923075X-RAY DIFFRACTION99
3.7792-4.01570.25261630.20023066X-RAY DIFFRACTION100
4.0157-4.32520.23661660.18383125X-RAY DIFFRACTION100
4.3252-4.75950.20771500.17093146X-RAY DIFFRACTION100
4.7595-5.4460.22551560.1743168X-RAY DIFFRACTION100
5.446-6.85290.2371770.19353186X-RAY DIFFRACTION100
6.8529-35.00130.22781840.19713381X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.8930.6979-0.27662.3555-0.55311.14990.14760.2985-0.01440.0089-0.00610.2416-0.0005-0.1511-0.09290.00480.0640.03070.20080.02030.2223-13.0107-2.0302111.7796
20.1704-1.3298-0.043.30350.07162.0203-0.1173-0.245-0.1454-0.07750.0414-0.1283-0.0389-0.21120.08620.0444-0.00390.05190.23290.00240.2694-4.88426.858566.3007
32.21480.471.27371.4068-0.4751.9006-0.1264-0.30350.2673-0.41360.1115-0.0140.0819-0.11310.05580.13720.01160.03810.0748-0.03660.1469-9.639-26.910664.1372
4-0.55910.4663-0.92111.98243.48737.3997-0.18550.0487-0.1296-0.0128-0.16390.0546-0.0506-0.98140.3860.2250.2145-0.06480.5106-0.12850.3299-5.4226-20.336190.1717
5-0.45280.6295-0.682.6973-2.8655.1311-0.1540.1089-0.0135-0.07060.1967-0.0194-0.1857-0.0782-0.02240.22740.02330.0010.53280.09210.2819-3.336416.644793.834
6-0.29190.6403-0.77526.15981.02332.0902-0.28010.0407-0.2211-0.25440.0596-0.31180.63190.11940.28240.3615-0.08420.12530.1905-0.03240.6154-0.95390.601960.7071
71.148-0.3931-0.33840.76820.61251.58350.51540.0537-0.0383-0.448-0.0281-0.09140.1170.0154-0.36791.31670.1716-0.26590.6013-0.12180.36425.6282-0.6913-16.5074
82.55880.8483-0.49652.613-0.86013.87970.00210.24410.0306-0.28070.02010.0326-0.9224-0.1584-0.08110.7556-0.03710.12660.5061-0.08010.336-1.40627.133429.2068
92.75181.1060.46355.9433-3.82476.95370.1815-0.04140.3488-1.26120.48540.82762.46450.6445-0.451.0485-0.1923-0.31750.48780.09890.36136.7897-26.48831.3791
10-0.6176-0.0147-0.07793.0265-0.76221.5020.5107-0.25820.2261-1.8123-0.134-0.3051-0.59291.110.44591.4607-0.6252-0.86991.15940.45590.2779-0.8549-20.36936.0559
110.3772-0.4409-0.43151.66841.41111.98490.3941-0.34570.0803-0.5932-0.1722-0.051-1.0752-0.6181-0.16681.33440.0428-0.07550.9012-0.13390.4566-3.78617.56721.7458
122.6945-1.5111-0.17382.0113-2.14553.6178-0.4073-0.045-0.5056-0.44290.0669-0.13220.4804-0.27450.22530.6293-0.10750.16050.3871-0.14350.5008-3.6460.790834.7538
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 I
7X-RAY DIFFRACTION7CHAIN X
8X-RAY DIFFRACTION8CHAIN Y
9X-RAY DIFFRACTION9CHAIN Z
10X-RAY DIFFRACTION10CHAIN U
11X-RAY DIFFRACTION11CHAIN V
12X-RAY DIFFRACTION12CHAIN W

+
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