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- PDB-2xdd: A processed non-coding RNA regulates a bacterial antiviral system -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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 / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
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.

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Experimental details

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Experiment

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

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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

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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

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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

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