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- PDB-5ycl: Crystal structure of HigBA complex from Shigella flexneri -

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Basic information

Entry
Database: PDB / ID: 5ycl
TitleCrystal structure of HigBA complex from Shigella flexneri
Components
  • Antitoxin HigA
  • mRNA interferase HigB
KeywordsSTRUCTURAL PROTEIN / Toxin / antitoxin system
Function / homology
Function and homology information


endonuclease activity / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / DNA binding / 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 HigB / Antitoxin HigA
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.101 Å
AuthorsYoun, W.S. / Seok, S.H. / Seo, M.D.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Structural changes of antitoxin HigA from Shigella flexneri by binding of its cognate toxin HigB.
Authors: Yoon, W.S. / Seok, S.H. / Won, H.S. / Cho, T. / Lee, S.J. / Seo, M.D.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,3894
Polymers54,3894
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-66 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.209, 78.209, 183.824
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 Antitoxin HigA


Mass: 15260.924 Da / Num. of mol.: 2 / Fragment: UNP residues 4-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: higA, SF3122, S3329 / Production host: Escherichia coli (E. coli) / References: UniProt: P67703
#2: Protein mRNA interferase HigB / Endoribonuclease HigB / Toxin HigB


Mass: 11933.328 Da / Num. of mol.: 2 / Fragment: UNP residues 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: higB, SF3123, S3330 / Production host: Escherichia coli (E. coli)
References: UniProt: P64580, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 % PEG 3350, 0.1 M HEPES pH 7.5, and 0.2 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.101→38.25 Å / Num. obs: 12386 / % possible obs: 100 % / Redundancy: 34.3 % / Net I/σ(I): 29.19

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155phasing
PHENIX1.10.1_2155data processing
HKL-2000data scaling
RefinementResolution: 3.101→38.25 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.48
RfactorNum. reflection% reflection
Rfree0.3029 1182 10.02 %
Rwork0.2679 --
obs0.2715 11801 95.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.101→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 0 5 3527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023592
X-RAY DIFFRACTIONf_angle_d0.6324871
X-RAY DIFFRACTIONf_dihedral_angle_d16.2712158
X-RAY DIFFRACTIONf_chiral_restr0.041571
X-RAY DIFFRACTIONf_plane_restr0.004621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1006-3.24170.38531520.31061368X-RAY DIFFRACTION100
3.2417-3.41260.38971470.32851365X-RAY DIFFRACTION99
3.4126-3.62630.44171240.37991122X-RAY DIFFRACTION82
3.6263-3.90610.41051350.37751220X-RAY DIFFRACTION88
3.9061-4.29890.2861400.25741237X-RAY DIFFRACTION91
4.2989-4.92040.25221600.1981403X-RAY DIFFRACTION100
4.9204-6.19670.25851590.2321408X-RAY DIFFRACTION100
6.1967-45.44410.22911650.22141496X-RAY DIFFRACTION100
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)
12.93271.6168-0.26533.48022.29976.4538-0.0068-0.09940.89520.01610.06910.9525-0.658-0.5272-0.07320.81940.2865-0.09210.4289-0.04440.5742-50.046934.1002-2.5173
21.02070.779-1.29650.8561-0.87021.70960.4030.53850.86010.01610.48420.18370.0159-0.5888-0.75940.3886-0.0663-0.21140.43640.16510.799-37.538235.92866.1194
36.66632.2754-1.00693.9117-1.31934.32270.490.02380.03560.6782-0.0077-0.53930.05120.0389-0.39730.3496-0.0415-0.17550.247-0.11180.5148-38.123327.364310.9766
42.0118-7.2067-1.17122.004-1.36750.67070.3710.04360.21820.1446-0.35-0.1663-0.18610.3655-0.03360.3473-0.0778-0.0920.25370.01650.4094-18.921527.918212.6379
55.83110.6543-3.55836.31-2.34991.9986-0.3488-0.55441.14820.0931-0.4286-0.39170.09010.52330.73470.14920.0401-0.06570.4144-0.0270.4686-15.198711.208117.3122
60.275-1.2696-0.58027.5118-0.14716.01930.1761-0.26380.18760.12080.1641-0.01310.26210.1878-0.28430.84070.54570.00090.39330.11690.5833-12.94265.000124.6683
74.649-0.22752.27841.4785-0.6571.31830.167-0.1047-0.09940.22580.0220.01360.42920.1597-0.1591.06210.6117-0.180.4530.11331.0853-7.41541.337721.098
81.4535-3.6849-1.8499.53343.48679.9144-0.32440.06860.1477-0.6527-0.17090.4646-0.05450.33880.48180.73990.0829-0.14670.6486-0.15031.4702-2.40174.318917.6042
98.75471.19282.70231.8114-2.21282.0024-0.1437-0.1896-0.4827-0.23970.0453-0.377-0.1511.19270.11840.46660.032-0.00770.6537-0.10710.8789-4.1889.460713.0499
103.285-1.96671.4054.68082.87754.54340.69750.7917-0.2359-0.4424-0.0717-0.3109-0.42670.1824-0.59060.97550.56380.18980.46910.18081.1112-12.9522-0.528211.2344
110.7183-0.12161.47352.698-2.6855.24560.66130.2841-0.4767-0.00390.28090.85060.0957-0.21-0.8660.40170.091-0.09170.3279-0.18030.9097-19.3233.05129.7964
123.7551-0.14891.32825.60740.80474.4873-0.2896-0.52810.20870.3456-0.5203-0.2736-0.00210.44950.81411.0923-0.04810.05750.9423-0.06190.599-11.869412.10520.9078
136.28311.55873.34155.01280.93986.2756-0.4430.08430.36850.07370.3751-0.5231-0.57670.15990.08080.247-0.0237-0.04170.1787-0.02680.476-26.443622.428417.2481
140.5574-0.844-0.87781.96130.71611.95620.01030.1204-0.2879-0.0608-0.5380.26170.16680.07280.228-0.0758-0.4297-0.34270.1131-0.38270.5861-21.673514.180318.3707
157.0608-1.7411-3.54764.7771.34585.3396-0.0472-0.9233-0.25740.5318-0.26740.76221.0168-0.3290.27350.4626-0.19980.03940.4634-0.10610.322-34.13939.056724.1755
162.70930.333-2.68476.52260.71532.83620.16730.0127-0.21020.38720.10520.33270.06840.0331-0.22560.25210.1252-0.03830.2855-0.08970.3745-30.887713.089421.8257
173.2823-0.2264-1.19472.91830.34158.01030.1345-0.5360.00750.026-0.50170.0023-0.80320.30480.28710.355-0.07250.09960.27610.01860.507-33.309718.481329.6128
184.426-0.3721-0.32825.3156-2.44971.3184-0.4502-0.1376-0.3120.5457-0.17141.42370.1312-1.34070.56470.2790.07420.00240.5244-0.11320.6517-52.721228.98815.4369
193.4672-1.1961-1.65935.037-2.60247.7124-0.1177-0.01140.19360.20970.2167-0.01960.2911-0.9634-0.10480.317-0.0762-0.05820.2999-0.08930.4164-43.527621.6232-8.5613
209.48651.1237-3.35375.6376-1.34534.4655-0.21490.2605-0.84970.2359-0.267-0.24410.72120.03940.43240.4805-0.0707-0.08790.2037-0.02920.58-33.76685.6766-12.9142
212.541.05911.16427.2236-2.18536.2925-0.05590.0967-0.8666-0.10520.20460.2083-0.19250.1683-0.17890.1980.09130.00020.4053-0.05440.5043-17.452811.3738-19.5094
225.12250.2629-1.49671.99910.58180.47810.29560.715-0.5283-0.583-0.5336-1.4120.0863-0.11570.19470.4374-0.09630.14351.1856-0.11270.8812-7.43197.9252-24.0571
231.3779-2.0704-2.80233.89192.37459.9354-0.2503-0.1237-0.7417-0.7275-0.4095-0.50160.47040.61940.61520.69640.3319-0.0340.5585-0.23691.0792-10.20992.0859-15.6536
241.36221.15241.65052.28512.46252.8627-0.05380.0241-0.47010.29330.2554-0.48890.40771.0597-0.16350.3750.02240.09381.0311-0.19951.2497-5.858314.8657-15.368
253.8163-2.8851.2993.29340.40672.177-0.6297-0.16530.9123-0.10740.96240.22180.5222-0.0918-0.34270.4903-0.0301-0.24440.71860.11760.5568-13.460313.8016-8.2799
264.78961.1470.48214.7510.90484.7133-0.30510.5459-0.3660.03220.3594-0.34990.47140.1091-0.01790.2718-0.0244-0.03640.2482-0.03640.37-28.195514.8588-18.403
273.5525-0.28683.38811.8449-0.0633.257-0.35120.85920.7678-0.2958-0.11950.1328-0.54940.67820.46540.4641-0.04490.17420.38750.05190.7173-26.274128.9471-24.3832
285.126-0.56271.30178.6934-1.11020.44150.4382-0.37710.6999-0.3778-0.3676-0.697-0.24170.0621-0.08590.1495-0.0559-0.03730.4041-0.00650.4858-27.464323.5742-21.9676
294.2372-1.70012.50962.8508-3.53737.70720.0872-0.12270.4745-0.4498-0.2483-0.28620.24250.03490.11220.258-0.02910.0450.119-0.01110.3454-34.891124.2594-28.3582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 26 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 63 )
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 90 )
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 95 )
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 100 )
8X-RAY DIFFRACTION8chain 'A' and (resid 101 through 105 )
9X-RAY DIFFRACTION9chain 'A' and (resid 106 through 118 )
10X-RAY DIFFRACTION10chain 'A' and (resid 119 through 129 )
11X-RAY DIFFRACTION11chain 'A' and (resid 130 through 136 )
12X-RAY DIFFRACTION12chain 'A' and (resid 137 through 141 )
13X-RAY DIFFRACTION13chain 'B' and (resid -1 through 16 )
14X-RAY DIFFRACTION14chain 'B' and (resid 17 through 43 )
15X-RAY DIFFRACTION15chain 'B' and (resid 44 through 56 )
16X-RAY DIFFRACTION16chain 'B' and (resid 57 through 78 )
17X-RAY DIFFRACTION17chain 'B' and (resid 79 through 99 )
18X-RAY DIFFRACTION18chain 'C' and (resid 4 through 17 )
19X-RAY DIFFRACTION19chain 'C' and (resid 18 through 63 )
20X-RAY DIFFRACTION20chain 'C' and (resid 64 through 76 )
21X-RAY DIFFRACTION21chain 'C' and (resid 77 through 91 )
22X-RAY DIFFRACTION22chain 'C' and (resid 92 through 103 )
23X-RAY DIFFRACTION23chain 'C' and (resid 104 through 119 )
24X-RAY DIFFRACTION24chain 'C' and (resid 120 through 129 )
25X-RAY DIFFRACTION25chain 'C' and (resid 130 through 140 )
26X-RAY DIFFRACTION26chain 'D' and (resid 0 through 43 )
27X-RAY DIFFRACTION27chain 'D' and (resid 44 through 56 )
28X-RAY DIFFRACTION28chain 'D' and (resid 57 through 78 )
29X-RAY DIFFRACTION29chain 'D' and (resid 79 through 99 )

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