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- PDB-5ydv: Regulatory domain of HypT from Salmonella typhimurium complexed w... -

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Basic information

Entry
Database: PDB / ID: 5ydv
TitleRegulatory domain of HypT from Salmonella typhimurium complexed with HOCl (HOCl-bound form)
ComponentsCell density-dependent motility repressor
KeywordsDNA BINDING PROTEIN / HypT / 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
hypochlorous acid / Cell density-dependent motility repressor / LysR family transcriptional regulator
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 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 14, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,0363
Polymers23,8871
Non-polymers1492
Water3,207178
1
A: Cell density-dependent motility repressor
hetero molecules

A: Cell density-dependent motility repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0726
Polymers47,7752
Non-polymers2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2530 Å2
ΔGint-48 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.293, 63.293, 101.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-560-

HOH

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Components

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


Mass: 23887.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HOCl (or hypochlorite ion) sulfate ion / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: qseD_2, DD95_15310, STMU2UK_04484 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J5DK07, UniProt: Q7CP75*PLUS
#2: Chemical ChemComp-8TR / hypochlorous acid


Mass: 52.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: ClHO
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 178 / 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: 42.16 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M lithium sulfate, 0.1M sodium cacodylate (pH 6.5), and 30%(v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 21030 / % possible obs: 98.1 % / Redundancy: 18.4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.012 / Net I/σ(I): 42.61
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.98 / Num. unique obs: 1032 / Rpim(I) all: 0.112 / % possible all: 99.4

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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: 1.752→19.48 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 23.26
RfactorNum. reflection% reflection
Rfree0.2532 1017 4.94 %
Rwork0.2087 --
obs0.2109 20597 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.752→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 7 178 1864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051727
X-RAY DIFFRACTIONf_angle_d0.7742342
X-RAY DIFFRACTIONf_dihedral_angle_d2.8721443
X-RAY DIFFRACTIONf_chiral_restr0.051258
X-RAY DIFFRACTIONf_plane_restr0.004306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.752-1.84430.28711390.25242447X-RAY DIFFRACTION87
1.8443-1.95970.2811400.23052835X-RAY DIFFRACTION99
1.9597-2.11090.28431440.22022857X-RAY DIFFRACTION100
2.1109-2.3230.26331460.2122862X-RAY DIFFRACTION100
2.323-2.65840.2321330.21252926X-RAY DIFFRACTION100
2.6584-3.34660.26231720.20452902X-RAY DIFFRACTION100
3.3466-19.48080.23051430.19192751X-RAY DIFFRACTION89
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)
11.71710.01750.78472.16270.18222.37210.16740.079-0.0765-0.3164-0.04460.04840.05760.05490.04240.06940.0475-0.04450.16720.04660.170240.292315.300337.8984
22.05390.1425-0.04251.50780.30011.99090.0310.0831-0.1148-0.2518-0.0146-0.06650.2094-0.2687-0.0420.03930.02310.02470.1608-0.02610.106126.417514.194519.964
33.03670.2626-1.46012.1156-0.83913.7487-0.0789-0.0606-0.2365-0.0653-0.1208-0.0378-0.0109-0.23980.10640.13260.06730.03660.14050.03730.090328.505317.939414.9905
41.28840.79581.29750.53171.19325.07850.2847-0.3113-0.21370.2289-0.2438-0.14380.5703-0.20560.05950.1375-0.065-0.0250.21530.09460.183732.312610.061542.004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 95 through 154 )
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 194 )
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 270 )
4X-RAY DIFFRACTION4chain 'A' and (resid 271 through 302 )

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