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- PDB-4mcx: P. vulgaris HIGBA structure, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 4mcx
TitleP. vulgaris HIGBA structure, crystal form 2
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 / antitoxin
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 / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains ...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 / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
E: Antidote protein
F: Killer protein


Theoretical massNumber of molelcules
Total (without water)73,8326
Polymers73,8326
Non-polymers00
Water3,657203
1
A: Antidote protein
B: Killer protein
C: Antidote protein
D: Killer protein


Theoretical massNumber of molelcules
Total (without water)49,2214
Polymers49,2214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-37 kcal/mol
Surface area17330 Å2
MethodPISA
2
E: Antidote protein
F: Killer protein

E: Antidote protein
F: Killer protein


Theoretical massNumber of molelcules
Total (without water)49,2214
Polymers49,2214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_875-x+3,-y+2,z1
Buried area7070 Å2
ΔGint-36 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.503, 120.503, 64.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11E-212-

HOH

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Components

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


Mass: 11549.950 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Strain: UR-75 / Gene: higA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7A224
#2: Protein Killer protein / / Host inhibition of growth B


Mass: 13060.770 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Strain: UR-75 / Gene: higB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7A225
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.77 %
Crystal growTemperature: 293.15 K / pH: 4.6
Details: 25% PEG 4000, 90 mM sodium acetate pH 4.6, 180 mM ammonium acetate, 4% acetone (w/v), 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-E / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011 / Details: MIRRORS
RadiationMonochromator: KOHZU DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→31 Å / Num. obs: 30863 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 34.75 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.3
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å30.79 Å
Translation2.5 Å30.79 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.3.0phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MCT

4mct


Resolution: 2.1→30.79 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 1242 4.56 %
Rwork0.173 --
obs0.174 27208 99.8 %
all-27208 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.98 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 0 203 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114486
X-RAY DIFFRACTIONf_angle_d1.1796053
X-RAY DIFFRACTIONf_dihedral_angle_d13.5541674
X-RAY DIFFRACTIONf_chiral_restr0.071670
X-RAY DIFFRACTIONf_plane_restr0.006778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28810.27521390.21942866X-RAY DIFFRACTION100
2.2881-2.39220.29911430.21862853X-RAY DIFFRACTION100
2.3922-2.51820.23631360.20242877X-RAY DIFFRACTION100
2.5182-2.67590.2431350.20052881X-RAY DIFFRACTION100
2.6759-2.88240.23291360.20262853X-RAY DIFFRACTION100
2.8824-3.17220.25991380.2012893X-RAY DIFFRACTION100
3.1722-3.63060.17781370.16742887X-RAY DIFFRACTION100
3.6306-4.57180.17781360.1372915X-RAY DIFFRACTION100
4.5718-30.79350.19011420.15362941X-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)
11.3375-0.36730.58642.2292-0.29460.72740.1523-0.13710.21650.1787-0.15640.0115-0.1011-0.06500.3535-0.04370.02570.3575-0.02810.277188.63897.059430.7633
24.06431.3731-0.48012.56420.12493.8991-0.0150.360.1645-0.32620.0050.2031-0.1433-0.38310.00090.36090.0644-0.01740.31970.03470.286488.3766105.715113.0867
31.0227-0.2984-0.48622.21890.77621.50830.1735-0.0248-0.17670.2483-0.03570.00150.2065-0.026900.3693-0.0522-0.01330.32990.00990.287192.718379.045431.0586
43.80481.84860.59182.50590.62314.6342-0.00780.2589-0.2569-0.12230.2008-0.3280.0150.33710.00180.29390.0089-0.01460.3257-0.07730.333693.456970.69313.3157
52.5650.24630.1131.5310.2420.61970.1289-0.2975-0.1014-0.0133-0.04940.1930.0058-0.093500.2431-0.0326-0.0050.29720.02410.2713113.27298.48579.2707
63.5307-1.2410.65573.0721-0.91872.83560.11490.3628-0.281-0.4429-0.04860.09210.22440.03670.00420.3179-0.0135-0.05310.2645-0.05790.2833105.520994.3239-8.3273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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