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- PDB-5yez: Regulatory domain of HypT M206Q mutant from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 5yez
TitleRegulatory domain of HypT M206Q mutant from Salmonella typhimurium
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


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 typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 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
C: Cell density-dependent motility repressor
D: Cell density-dependent motility repressor


Theoretical massNumber of molelcules
Total (without water)95,5374
Polymers95,5374
Non-polymers00
Water0
1
A: Cell density-dependent motility repressor
B: Cell density-dependent motility repressor


Theoretical massNumber of molelcules
Total (without water)47,7682
Polymers47,7682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-23 kcal/mol
Surface area18190 Å2
MethodPISA
2
C: Cell density-dependent motility repressor
D: Cell density-dependent motility repressor


Theoretical massNumber of molelcules
Total (without water)47,7682
Polymers47,7682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-18 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.204, 67.326, 192.255
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: 23884.186 Da / Num. of mol.: 4 / Mutation: M206Q
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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J5DK07, UniProt: Q7CP75*PLUS

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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: 1.73 Å3/Da / Density % sol: 29.08 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate (pH 5.6) 2 % (v/v) tacsimate (pH 5.0), and 18% (v/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20398 / % possible obs: 95.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.029 / Net I/σ(I): 18.72
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.7 % / Num. unique obs: 933 / Rpim(I) all: 0.239 / % possible all: 90.3

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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: 2.6→49.479 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.77
RfactorNum. reflection% reflection
Rfree0.2907 904 4.84 %
Rwork0.2337 --
obs0.2366 18684 87.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 0 0 5988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036113
X-RAY DIFFRACTIONf_angle_d0.5518273
X-RAY DIFFRACTIONf_dihedral_angle_d7.8043674
X-RAY DIFFRACTIONf_chiral_restr0.04922
X-RAY DIFFRACTIONf_plane_restr0.0031065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.76310.3421890.29581722X-RAY DIFFRACTION52
2.7631-2.97640.34251320.27992808X-RAY DIFFRACTION85
2.9764-3.27590.30031420.26373126X-RAY DIFFRACTION94
3.2759-3.74970.31371830.24083253X-RAY DIFFRACTION97
3.7497-4.72370.25471780.20183335X-RAY DIFFRACTION99
4.7237-49.48810.27871800.2173536X-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)
16.90140.68730.05243.2225-0.43132.2963-0.1386-0.02150.23330.19770.2148-0.19170.03590.0987-0.10290.4477-0.0293-0.09120.04340.02310.17775.722-11.4368-21.56
21.3358-0.2232-0.28241.2036-0.38610.33160.0780.2026-0.43450.2978-0.02160.12750.2908-0.06770.02630.3618-0.0259-0.01890.0587-0.13990.1518-3.9871-21.1061-26.699
34.9949-1.1969-2.41462.19891.03264.49090.09430.45250.0522-0.1137-0.2580.32550.318-0.17690.17170.11030.07690.02550.1670.01920.1816-15.1435-5.6822-38.7514
41.46920.06990.79350.13050.28490.9204-0.04810.01020.12660.21510.10240.3060.0671-0.0114-0.05890.31870.0503-0.0052-0.02830.07930.1302-0.4137-20.2916-17.3166
53.18010.4877-1.13792.93591.15434.73120.33570.42050.02050.0406-0.12710.0621-0.03450.3677-0.09920.3206-0.01510.00280.3723-0.01770.02045.8815-3.2832-48.6326
62.6244-0.2542-0.52533.19160.42122.9134-0.02730.06230.2389-0.20610.01260.08180.07630.1774-0.10840.16080.06850.0270.0077-0.04620.101613.00373.999-25.2554
77.61862.12715.59442.07981.19294.3105-0.27380.16280.445-0.59760.21730.2028-0.3292-0.55650.0790.38270.04750.05440.36240.07250.216.80632.8847-54.0567
83.62131.5034-1.69396.49951.43461.9990.04150.36480.2889-0.39620.456-0.0795-0.13840.1754-0.41170.3744-0.08380.02630.5192-0.06960.298614.0285-35.3208-3.3232
92.0289-0.276-0.07254.0529-0.59721.05560.2359-0.00030.6272-0.6117-0.2447-0.28710.0109-0.119-0.02350.28260.03610.01170.0105-0.18440.305619.2991-39.1476-27.0329
102.0462-0.7024-1.42651.9151-1.51965.55540.1231-0.3030.0480.44220.09370.1184-0.26110.0038-0.52180.124-0.0939-0.03720.1975-0.0810.38938.7245-34.039-9.5124
115.7728-0.4624-0.59930.985-0.37591.5202-0.2046-1.05350.84280.1107-0.15670.0982-0.4055-0.09280.28150.32080.0321-0.28550.6592-0.06671.021833.9482-43.1926-19.5184
120.19780.252-0.10222.92432.10351.9678-0.2311-0.6571-0.35480.31270.3048-0.5266-0.04060.8908-0.10750.38850.08750.0180.5365-0.07740.547938.4913-39.4937-17.9266
131.8588-0.61490.38522.8677-0.4377.7276-0.09130.7791-0.2269-0.0734-0.07080.05860.17190.48050.18910.2918-0.16750.05060.57-0.10320.233530.2775-23.8196-5.3263
141.67240.5495-0.59473.4471.51891.0961-0.19360.1051-0.6385-0.35570.653-0.8257-0.02120.4371-0.35140.3227-0.1095-0.00980.7217-0.18390.457543.9218-39.9499-16.6019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 98 through 135 )
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 270 )
4X-RAY DIFFRACTION4chain 'A' and (resid 271 through 300 )
5X-RAY DIFFRACTION5chain 'B' and (resid 100 through 167 )
6X-RAY DIFFRACTION6chain 'B' and (resid 168 through 270 )
7X-RAY DIFFRACTION7chain 'B' and (resid 271 through 302 )
8X-RAY DIFFRACTION8chain 'C' and (resid 102 through 170 )
9X-RAY DIFFRACTION9chain 'C' and (resid 171 through 258 )
10X-RAY DIFFRACTION10chain 'C' and (resid 259 through 298 )
11X-RAY DIFFRACTION11chain 'D' and (resid 100 through 120 )
12X-RAY DIFFRACTION12chain 'D' and (resid 121 through 179 )
13X-RAY DIFFRACTION13chain 'D' and (resid 180 through 263 )
14X-RAY DIFFRACTION14chain 'D' and (resid 264 through 300 )

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