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- PDB-9chn: P. vulgaris trimeric HigBA- operator 2 DNA -

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Basic information

Entry
Database: PDB / ID: 9chn
TitleP. vulgaris trimeric HigBA- operator 2 DNA
Components
  • Antitoxin HigA
  • DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')
  • DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')
  • Endoribonuclease HigB
KeywordsANTITOXIN/DNA BINDING PROTEIN/DNA / Toxin / antitoxin / promoter / DNA BINDING PROTEIN / ANTITOXIN-DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


toxin sequestering activity / plasmid maintenance / RNA catabolic process / translation repressor activity / RNA endonuclease activity / negative regulation of cell growth / ribosome binding / Hydrolases; Acting on ester bonds / transcription cis-regulatory region binding / negative regulation of translation ...toxin sequestering activity / plasmid maintenance / RNA catabolic process / translation repressor activity / RNA endonuclease activity / negative regulation of cell growth / ribosome binding / Hydrolases; Acting on ester bonds / transcription cis-regulatory region binding / negative regulation of translation / protein heterodimerization activity / DNA-binding transcription factor activity / negative regulation of cell population proliferation / mRNA binding / regulation of DNA-templated transcription
Similarity search - Function
Toxin HigB-1 / RelE-like toxin of type II toxin-antitoxin system HigB / Toxin-antitoxin system, antidote protein, HigA / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitoxin HigA / Endoribonuclease HigB
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPavelich, I.J. / Schureck, M.A. / Hoffer, E.D. / Dunham, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
Other private United States
Other government United States
CitationJournal: To Be Published
Title: P. vulgaris trimeric HigBA- operator 2 DNA
Authors: Pavelich, I.J. / Schureck, M.A. / Hoffer, E.D. / Dunham, C.M.
History
DepositionJul 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin HigA
B: Endoribonuclease HigB
C: Antitoxin HigA
D: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')
E: DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,16317
Polymers46,8725
Non-polymers29212
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.820, 139.820, 80.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 2 types, 3 molecules ACB

#1: Protein Antitoxin HigA / Antidote protein / Host inhibition of growth protein A


Mass: 11549.950 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: higA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A224
#2: Protein Endoribonuclease HigB / Host inhibition of growth protein B / Killer protein / Toxin HigB / mRNA interferase HigB


Mass: 10889.403 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: higB / Production host: Escherichia coli (E. coli)
References: UniProt: Q7A225, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 2 molecules DE

#3: DNA chain DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')


Mass: 6390.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Proteus vulgaris (bacteria)
#4: DNA chain DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')


Mass: 6492.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Proteus vulgaris (bacteria)

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Non-polymers , 2 types, 183 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 4.55 Å3/Da / Density % sol: 72.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Tris-HCl, KCl, MgCl2, 2-mercaptoethanol, NaCl, EDTA, CaCl2, PEG 3350
PH range: 7.5-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→34.98 Å / Num. obs: 23989 / % possible obs: 99.7 % / Redundancy: 7.209 % / Biso Wilson estimate: 77.144 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.061 / Χ2: 1.042 / Net I/σ(I): 18.53 / Num. measured all: 172942 / Scaling rejects: 91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.677.0971.0181.9412250175117260.8671.09898.6
2.67-2.747.3030.7662.6512832176017570.9380.82599.8
2.74-2.827.2920.5593.6111770161616140.9650.60299.9
2.82-2.917.3070.4434.3511969163916380.9760.47799.9
2.91-37.3060.3375.6211631159315920.9840.36399.9
3-3.117.2970.2128.0711098152515210.9930.22999.7
3.11-3.237.2750.12311.5610825149114880.9980.13299.8
3.23-3.367.2870.06815.610325142414170.9990.07399.5
3.36-3.517.2540.06318.819793135113500.9990.06899.9
3.51-3.687.2210.05721.79510132113170.9990.06199.7
3.68-3.887.2590.0623.68871122212220.9990.065100
3.88-4.117.1820.04929.078482118111810.9990.053100
4.11-4.47.2070.04534.147935110111010.9990.048100
4.4-4.757.1880.04336.077612105910590.9990.047100
4.75-5.27.1260.04138.2367349459450.9990.045100
5.2-5.827.0670.04240.6860428558550.9990.045100
5.82-6.717.0880.03942.6555007767760.9990.042100
6.71-8.227.0510.03445.4645836506500.9990.037100
8.22-11.636.9120.03247.7834705035020.9990.03499.8
11.63-34.986.1510.03444.8317102902780.9980.03895.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MCX

4mcx


Resolution: 2.8→34.98 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 1841 10.08 %
Rwork0.174 16418 -
obs0.1783 18259 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 242.3 Å2 / Biso mean: 69.9751 Å2 / Biso min: 28.14 Å2
Refinement stepCycle: final / Resolution: 2.8→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 855 12 171 3180
Biso mean--78.58 59.55 -
Num. residues----314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.880.3382950.285790299768
2.88-2.960.29071230.25411009113278
2.96-3.060.27691310.24641192132389
3.06-3.160.2751480.24261282143097
3.17-3.290.25361490.20313331482100
3.29-3.440.22891520.1761304145699
3.44-3.620.24631480.179113271475100
3.62-3.850.21491440.181213211465100
3.85-4.140.19781450.15813341479100
4.15-4.560.1651500.136113421492100
4.56-5.220.13861470.136513521499100
5.22-6.560.21621520.153913321484100
6.58-34.980.23531570.16861388154599
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)
18.60031.6946-2.31241.8304-1.031.1698-0.0530.89140.0023-0.2160.06790.0340.1069-0.3813-0.03010.30320.0257-0.03250.2856-0.02530.549326.983-4.4068-13.8709
21.2685-0.52420.04486.27020.36328.75750.02211.8222-0.5082-1.1170.07370.26720.4027-0.3844-0.11370.8316-0.0797-0.04141.4835-0.29670.723922.0034-9.2634-32.0964
33.5650.3934-0.01360.18680.15060.63360.0558-0.0992-0.8568-0.0984-0.16890.10820.24710.10630.13680.31880.0339-0.0150.2707-0.00360.836344.7023-7.3218-10.1961
46.3491-1.6825-1.43030.3413-0.0962-0.3154-0.3395-0.90970.36370.15930.1475-0.06090.06140.21830.17280.32530.0209-0.03380.7094-0.0230.737834.18620.96314.3908
55.92990.1112-0.10160.1104-0.40531.1152-0.3132-1.4165-0.22330.13180.1452-0.18020.08870.33530.08990.31160.0665-0.0430.6333-0.08420.804834.98991.00484.5081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:95)A1 - 95
2X-RAY DIFFRACTION2(chain B and resseq 0:91)B0 - 91
3X-RAY DIFFRACTION3(chain C and resseq 7:91)C7 - 91
4X-RAY DIFFRACTION4(chain D and resseq 1:21)D1 - 21
5X-RAY DIFFRACTION5(chain E and resseq 1:21)E1 - 21

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