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- PDB-5ifg: Crystal structure of HigA-HigB complex from E. Coli -

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Basic information

Entry
Database: PDB / ID: 5ifg
TitleCrystal structure of HigA-HigB complex from E. Coli
Components
  • Antitoxin HigA
  • mRNA interferase HigB
KeywordsHYDROLASE/ANTITOXIN / mRNA interferase / HYDROLASE-ANTITOXIN complex
Function / homology
Function and homology information


toxin-antitoxin complex / regulation of growth / core promoter sequence-specific DNA binding / regulation of mRNA stability / RNA endonuclease activity / Hydrolases; Acting on ester bonds / negative regulation of translation / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding
Similarity search - Function
Toxin-antitoxin system, mRNA interferase HigB / HigB_toxin, RelE-like toxic component of a toxin-antitoxin system / Antitoxin HigA / 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
mRNA interferase toxin HigB / Antitoxin HigA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.702 Å
AuthorsYang, J.S. / Zhou, K. / Gao, z.Q. / Liu, Q.S. / Dong, Y.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: Structural insight into the E. coli HigBA complex
Authors: Yang, J. / Zhou, K. / Liu, P. / Dong, Y. / Gao, Z. / Zhang, J. / Liu, Q.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA interferase HigB
B: Antitoxin HigA
C: mRNA interferase HigB
D: Antitoxin HigA


Theoretical massNumber of molelcules
Total (without water)55,0194
Polymers55,0194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-59 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.924, 77.924, 180.634
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein mRNA interferase HigB / hypothesis mRNA interferase HigB / Endoribonuclease HigB / Toxin HigB


Mass: 12266.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: higB, ygjN, b3083, JW3054 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P64578, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin HigA / hypothesis mRNA interferase HigA


Mass: 15242.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: higA, ygjM, b3082, JW3053 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P67701

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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: 2.88 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 0.2M (NH4)2SO4, 0.1M Bis-Tris pH5.3, 20%(w/v) PEG3350, 0.01M KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.33
ReflectionResolution: 2.7→50 Å / Num. obs: 35954 / % possible obs: 99.2 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 65.78
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 20.9 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 14.67 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.702→44.928 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.79 / Stereochemistry target values: TWIN_LSQ_F
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1710 5.14 %random selection
Rwork0.1985 ---
obs0.2019 33261 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.702→44.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 0 0 3408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133479
X-RAY DIFFRACTIONf_angle_d1.6684700
X-RAY DIFFRACTIONf_dihedral_angle_d17.931268
X-RAY DIFFRACTIONf_chiral_restr0.067535
X-RAY DIFFRACTIONf_plane_restr0.006598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7029-2.78240.36911470.3072658X-RAY DIFFRACTION94
2.7824-2.87210.36971370.30372641X-RAY DIFFRACTION95
2.8721-2.97470.28821420.28122613X-RAY DIFFRACTION95
2.9747-3.09370.28481360.26412679X-RAY DIFFRACTION95
3.0937-3.23430.28811650.24492607X-RAY DIFFRACTION94
3.2343-3.40460.22021730.22152650X-RAY DIFFRACTION94
3.4046-3.61760.24871250.21492627X-RAY DIFFRACTION94
3.6176-3.89630.21311190.20372678X-RAY DIFFRACTION95
3.8963-4.28730.18611510.17252637X-RAY DIFFRACTION94
4.2873-4.90520.18721440.14332644X-RAY DIFFRACTION95
4.9052-6.17070.21491450.17072639X-RAY DIFFRACTION95
6.1707-29.4370.22761240.17482433X-RAY DIFFRACTION87

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