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- PDB-4mct: P. vulgaris HIGBA structure, crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 4mct
TitleP. vulgaris HIGBA structure, crystal form 1
Components
  • Antidote protein
  • Killer protein
KeywordsTOXIN / bacterial toxins / biofilms / cell metabolism / energy metabolism / helix-turn-helix transcription factors / microbial pathogenesis / stress response / stringent response / transcription repressor / translation control
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 / negative regulation of translation / transcription cis-regulatory region binding ...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 / negative regulation of translation / transcription cis-regulatory region binding / 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 / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. ...Toxin HigB-1 / RelE-like toxin of type II toxin-antitoxin system HigB / Toxin-antitoxin system, antidote protein, HigA / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Antitoxin HigA / Endoribonuclease HigB
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSchureck, M.A. / Maehigashi, T. / Dunham, C.M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of the Proteus vulgaris HigB-(HigA)2-HigB Toxin-Antitoxin Complex.
Authors: Schureck, M.A. / Maehigashi, T. / Miles, S.J. / Marquez, J. / Cho, S.E. / Erdman, R. / Dunham, C.M.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antidote protein
B: Killer protein
C: Antidote protein
D: Killer protein


Theoretical massNumber of molelcules
Total (without water)50,0054
Polymers50,0054
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-31 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.860, 94.860, 126.814
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-203-

HOH

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Components

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


Mass: 14019.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Strain: UR-75 / Gene: higA / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7A224
#2: Protein Killer protein / Host inhibition of growth B


Mass: 10983.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Strain: UR-75 / Gene: higB / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7A225
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 293.15 K / pH: 7.5
Details: 3-10 % PEG 3350, 0.2 M L-proline, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97922
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2011 / Details: MIRRORS
RadiationMonochromator: KOHZU DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionRedundancy: 6.6 % / Number: 125944 / Rmerge(I) obs: 0.163 / Χ2: 1.81 / D res high: 2.7 Å / D res low: 40 Å / Num. obs: 18970 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.314010010.0774.9576.3
5.817.3110010.1122.746.5
5.085.8110010.132.7376.7
4.625.0810010.1252.8636.8
4.284.6210010.132.9296.9
4.034.2810010.1432.5586.9
3.834.0310010.1532.1427
3.663.8310010.2091.7327
3.523.6610010.2382.5367
3.43.5210010.2551.4647.1
3.33.410010.2981.2587.1
3.23.310010.361.1137.1
3.123.210010.4090.9977.1
3.043.1210010.5120.9137
2.973.0410010.6210.7816.9
2.912.9710010.6250.7796.6
2.852.9110010.7670.6666.3
2.82.8510010.9260.6365.9
2.752.899.910.6645.5
2.72.7599.110.8960.6544.9
ReflectionResolution: 2.8→40 Å / Num. obs: 35400 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 63.46 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 13.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.1 / % possible all: 97.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSol1.7.2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→41.08 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 3139 10.02 %
Rwork0.197 --
obs0.201 31336 99.7 %
all-35400 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 0 40 2983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012999
X-RAY DIFFRACTIONf_angle_d1.3194047
X-RAY DIFFRACTIONf_dihedral_angle_d13.9331119
X-RAY DIFFRACTIONf_chiral_restr0.053447
X-RAY DIFFRACTIONf_plane_restr0.007520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.84390.33921410.28051282X-RAY DIFFRACTION99
2.8439-2.89050.31121400.27781310X-RAY DIFFRACTION100
2.8905-2.94040.35871620.26521274X-RAY DIFFRACTION100
2.9404-2.99380.33631460.26611257X-RAY DIFFRACTION100
2.9938-3.05140.31861380.25011317X-RAY DIFFRACTION100
3.0514-3.11360.26771420.23861220X-RAY DIFFRACTION100
3.1136-3.18130.31731380.23681315X-RAY DIFFRACTION100
3.1813-3.25530.24531500.22031295X-RAY DIFFRACTION100
3.2553-3.33670.32841380.23171235X-RAY DIFFRACTION100
3.3367-3.42680.27921460.20521327X-RAY DIFFRACTION100
3.4268-3.52760.27031550.2071259X-RAY DIFFRACTION100
3.5276-3.64140.24111420.211305X-RAY DIFFRACTION100
3.6414-3.77150.24831420.20281270X-RAY DIFFRACTION100
3.7715-3.92240.28621480.21285X-RAY DIFFRACTION100
3.9224-4.10070.22761340.19051284X-RAY DIFFRACTION100
4.1007-4.31670.23451440.17151293X-RAY DIFFRACTION100
4.3167-4.58680.20861360.15441250X-RAY DIFFRACTION100
4.5868-4.94040.17011460.15991315X-RAY DIFFRACTION100
4.9404-5.43660.17471290.17351286X-RAY DIFFRACTION100
5.4366-6.2210.22991500.18861270X-RAY DIFFRACTION100
6.221-7.82890.24721370.20021295X-RAY DIFFRACTION100
7.8289-41.08020.18191350.17611253X-RAY DIFFRACTION97

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