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- PDB-5yer: Regulatory domain of HypT from Salmonella typhimurium (Bromide io... -

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Basic information

Entry
Database: PDB / ID: 5yer
TitleRegulatory domain of HypT from Salmonella typhimurium (Bromide ion-bound)
ComponentsCell density-dependent motility repressor
KeywordsDNA BINDING PROTEIN / HOCl / HOCl-specific transcription factor / LysR-type transcription regulator / Hypochlorous acid / hypochlorite / regulatory domain
Function / homology
Function and homology information


amino acid biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
BROMIDE ION / Cell density-dependent motility repressor / LysR family transcriptional regulator
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsJo, I. / Hong, S. / Ahn, J. / Ha, N.C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structural basis for HOCl recognition and regulation mechanisms of HypT, a hypochlorite-specific transcriptional regulator.
Authors: Jo, I. / Kim, D. / No, T. / Hong, S. / Ahn, J. / Ryu, S. / Ha, N.C.
History
DepositionSep 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 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
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell density-dependent motility repressor
B: Cell density-dependent motility repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2868
Polymers47,7752
Non-polymers5126
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-49 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.142, 64.121, 100.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell density-dependent motility repressor / Quorum-sensing regulator protein D


Mass: 23887.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: qseD_2, DD95_15310, STMU2UK_04484 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0J5DK07, UniProt: Q7CP75*PLUS
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium sulfate, 0.1M sodium cacodylate (pH 6.5), 0.15M NaBr, 28%(v/v) PEG400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18048 / % possible obs: 96 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.033 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
2.3-2.342.60.2552.867160.6760.15577.3
2.34-2.383.10.2713.178430.6950.15491.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YDO

5ydo


Resolution: 2.301→41.062 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.2607 1682 9.97 %
Rwork0.2095 --
obs0.2147 16679 89.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.301→41.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 14 63 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023414
X-RAY DIFFRACTIONf_angle_d0.474629
X-RAY DIFFRACTIONf_dihedral_angle_d4.8682055
X-RAY DIFFRACTIONf_chiral_restr0.04512
X-RAY DIFFRACTIONf_plane_restr0.003602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3009-2.33680.2879580.2435583X-RAY DIFFRACTION41
2.3368-2.37510.3266840.2698832X-RAY DIFFRACTION58
2.3751-2.41610.38131080.2703981X-RAY DIFFRACTION68
2.4161-2.460.28831200.2761026X-RAY DIFFRACTION72
2.46-2.50730.32191290.26941089X-RAY DIFFRACTION77
2.5073-2.55850.35381410.2551231X-RAY DIFFRACTION86
2.5585-2.61410.30311430.2471241X-RAY DIFFRACTION88
2.6141-2.67490.33371360.24951341X-RAY DIFFRACTION92
2.6749-2.74180.34751620.24921402X-RAY DIFFRACTION97
2.7418-2.81590.27251620.24391391X-RAY DIFFRACTION98
2.8159-2.89880.2831640.23331415X-RAY DIFFRACTION98
2.8988-2.99230.28961540.23881401X-RAY DIFFRACTION99
2.9923-3.09920.27221590.23481400X-RAY DIFFRACTION99
3.0992-3.22330.27261550.22011437X-RAY DIFFRACTION99
3.2233-3.36990.25351610.22191405X-RAY DIFFRACTION99
3.3699-3.54750.23121650.20161420X-RAY DIFFRACTION100
3.5475-3.76960.23731430.19851439X-RAY DIFFRACTION100
3.7696-4.06040.24561610.17331431X-RAY DIFFRACTION100
4.0604-4.46860.2571610.16951423X-RAY DIFFRACTION100
4.4686-5.11410.20211480.15151434X-RAY DIFFRACTION100
5.1141-6.43930.20671610.19311443X-RAY DIFFRACTION100
6.4393-41.06890.21161480.18631421X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.8639 Å / Origin y: 40.5793 Å / Origin z: 37.8604 Å
111213212223313233
T0.0539 Å20.015 Å2-0.0116 Å2-0.0497 Å2-0.0302 Å2--0.0668 Å2
L0.2998 °2-0.0177 °20.3063 °2-0.0714 °20.0233 °2--0.4954 °2
S0.0364 Å °-0.0218 Å °-0.0081 Å °-0.0325 Å °0.0265 Å °0.0382 Å °0.0504 Å °0.0954 Å °0.0793 Å °
Refinement TLS groupSelection details: all

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