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- PDB-5ydo: Regulatory domain of HypT from Salmonella typhimurium (apo-form) -

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Basic information

Entry
Database: PDB / ID: 5ydo
TitleRegulatory domain of HypT from Salmonella typhimurium (apo-form)
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 / DNA binding
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
Cell density-dependent motility repressor / LysR family transcriptional regulator
Similarity search - Component
Biological speciesSalmonella choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 13, 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Cell density-dependent motility repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9832
Polymers23,8871
Non-polymers961
Water1,946108
1
A: Cell density-dependent motility repressor
hetero molecules

A: Cell density-dependent motility repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9674
Polymers47,7752
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2470 Å2
ΔGint-48 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.344, 63.344, 100.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cell density-dependent motility repressor / HTH-type transcriptional regulator YjiE / LysR family transcriptional regulator


Mass: 23887.254 Da / Num. of mol.: 1 / Fragment: UNP residues 97-302
Source method: isolated from a genetically manipulated source
Details: Sulfate ion / Source: (gene. exp.) Salmonella choleraesuis (bacteria)
Gene: yjiE_2, A7S24_17855, A7S72_19140, IN36_08870, IN69_18165, NGUA18_03006
Plasmid: pProEx-HTa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M0PNP4, UniProt: Q7CP75*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM ammonium sulfate, 50mM Bis-Tris (pH 6.5), 30%(v/v) pentaerythritol ethoxylate (15/4 EO/OH), and 2mM TCEP.

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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 315 / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14482 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 16.5 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.013 / Net I/σ(I): 41.23
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.29 / Num. unique obs: 677 / Rpim(I) all: 0.061 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DENZOdata reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→39.441 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 23.88
RfactorNum. reflection% reflection
Rfree0.2536 736 5.21 %
Rwork0.2043 --
obs0.2069 14127 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 5 108 1792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031719
X-RAY DIFFRACTIONf_angle_d0.5532331
X-RAY DIFFRACTIONf_dihedral_angle_d3.1161035
X-RAY DIFFRACTIONf_chiral_restr0.041257
X-RAY DIFFRACTIONf_plane_restr0.003304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.15460.29571320.24312405X-RAY DIFFRACTION90
2.1546-2.37140.31931340.23532675X-RAY DIFFRACTION99
2.3714-2.71450.28891630.23112687X-RAY DIFFRACTION100
2.7145-3.41970.26821500.21472744X-RAY DIFFRACTION100
3.4197-39.44860.2041570.16882880X-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)
11.9454-0.01820.78721.6092-0.25052.75310.1577-0.02470.0371-0.2594-0.02840.09630.09320.0249-0.07260.08840.0632-0.05570.14210.03740.201440.677215.218837.7065
21.930.01180.62380.56070.8791.56750.012-0.2102-0.2860.13190.0201-0.05750.5216-0.31-0.14590.1369-0.01870.01070.21110.02350.171129.13018.065229.0313
32.57130.1087-0.87562.2444-0.51091.9492-0.01390.0399-0.0847-0.2058-0.15770.0343-0.1091-0.34750.08390.13160.09120.00470.20930.01830.080427.463519.104413.1345
41.13910.87581.10761.07641.98314.24180.1564-0.3673-0.13470.318-0.262-0.11390.5017-0.47560.0340.1641-0.06620.00480.26650.08370.195432.396810.069841.7669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 94 through 154 )
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 179 )
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 270 )
4X-RAY DIFFRACTION4chain 'A' and (resid 271 through 302 )

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