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- PDB-6irp: Crystal structure of HigA from Shigella flexneri -

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Basic information

Entry
Database: PDB / ID: 6irp
TitleCrystal structure of HigA from Shigella flexneri
ComponentsAntitoxin HigA
KeywordsANTITOXIN / Antoxin
Function / homologyAntitoxin 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 / core promoter sequence-specific DNA binding / regulation of DNA-templated transcription / Antitoxin HigA
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.954 Å
AuthorsYoon, 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
DepositionNov 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antitoxin HigA
B: Antitoxin HigA


Theoretical massNumber of molelcules
Total (without water)30,4862
Polymers30,4862
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-25 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.366, 80.366, 90.385
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

21A-262-

HOH

31A-268-

HOH

41B-203-

HOH

51B-265-

HOH

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Components

#1: Protein Antitoxin HigA


Mass: 15242.830 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.1M HEPES pH 7.5 , 0.2 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
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: 1.95→50 Å / Num. obs: 24365 / % possible obs: 100 % / Redundancy: 11.9 % / Net I/σ(I): 5.4
Reflection shellResolution: 1.95→1.98 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155phasing
HKL-2000data scaling
RefinementResolution: 1.954→34.799 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.04
RfactorNum. reflection% reflection
Rfree0.2306 1998 8.21 %
Rwork0.2058 --
obs0.2079 24325 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.954→34.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 0 157 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072120
X-RAY DIFFRACTIONf_angle_d0.8352876
X-RAY DIFFRACTIONf_dihedral_angle_d111302
X-RAY DIFFRACTIONf_chiral_restr0.047344
X-RAY DIFFRACTIONf_plane_restr0.005370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9542-2.00310.29671400.23281568X-RAY DIFFRACTION99
2.0031-2.05730.26381390.22621581X-RAY DIFFRACTION100
2.0573-2.11780.27251400.20431603X-RAY DIFFRACTION100
2.1178-2.18610.17841390.2021556X-RAY DIFFRACTION100
2.1861-2.26430.24271420.20251593X-RAY DIFFRACTION100
2.2643-2.35490.22441410.19141601X-RAY DIFFRACTION100
2.3549-2.4620.23641430.20231577X-RAY DIFFRACTION100
2.462-2.59180.25321430.20811617X-RAY DIFFRACTION100
2.5918-2.75410.24761420.20951588X-RAY DIFFRACTION100
2.7541-2.96670.20331430.21071596X-RAY DIFFRACTION100
2.9667-3.2650.24131460.21031583X-RAY DIFFRACTION100
3.265-3.7370.21731460.20251611X-RAY DIFFRACTION100
3.737-4.70640.18731430.18011631X-RAY DIFFRACTION100
4.7064-34.8050.26631510.22891622X-RAY DIFFRACTION98

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