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- PDB-5ydw: Full-length structure of HypT from Salmonella typhimuriuma (hypoc... -

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Basic information

Entry
Database: PDB / ID: 5ydw
TitleFull-length structure of HypT from Salmonella typhimuriuma (hypochlorite-specific LysR-type transcriptional regulator)
ComponentsCell density-dependent motility repressor
KeywordsDNA BINDING PROTEIN / HOCl / HOCl-specific transcription factor / LysR-type transcription regulator / Hypochlorous acid / hypochlorite
Function / homology
Function and homology information


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
Cell density-dependent motility repressor / LysR family transcriptional regulator
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 15, 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


Theoretical massNumber of molelcules
Total (without water)69,3972
Polymers69,3972
Non-polymers00
Water00
1
A: Cell density-dependent motility repressor
B: Cell density-dependent motility repressor

A: Cell density-dependent motility repressor
B: Cell density-dependent motility repressor


Theoretical massNumber of molelcules
Total (without water)138,7944
Polymers138,7944
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area15370 Å2
ΔGint-86 kcal/mol
Surface area51450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.606, 114.556, 128.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 34698.500 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(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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium acetate, 0.1M MES (pH 6.5), 30%(v/v) PEG400, 2mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9999 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: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 9592 / % possible obs: 95 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.061 / Net I/σ(I): 8.3
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 460 / Rpim(I) all: 0.244 / % possible all: 95.8

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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: 3.3→19.674 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 30.88
RfactorNum. reflection% reflection
Rfree0.2977 394 4.72 %
Rwork0.2512 --
obs0.2536 8343 83.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4716 0 0 0 4716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034811
X-RAY DIFFRACTIONf_angle_d0.5466509
X-RAY DIFFRACTIONf_dihedral_angle_d5.4552909
X-RAY DIFFRACTIONf_chiral_restr0.04722
X-RAY DIFFRACTIONf_plane_restr0.004850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.77480.3216910.30671724X-RAY DIFFRACTION55
3.7748-4.74480.28051290.25183053X-RAY DIFFRACTION97
4.7448-19.67390.29851740.22793172X-RAY DIFFRACTION98
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)
11.3515-1.9290.26744.40551.70744.3380.0215-0.0204-0.36350.1404-0.29750.99150.1134-0.5598-0.23260.40830.08470.01130.1410.06510.5846-35.9186-28.511921.9461
23.70741.0334-1.22591.49410.01182.98570.76830.39950.6596-0.2424-0.24730.2699-0.0938-0.54870.1970.41880.25810.00320.41380.06320.2684-32.8464-18.782617.4257
32.2212-1.43321.19951.1733-1.24991.9504-0.107-0.07770.35930.27690.0306-0.1326-0.18020.1290.03450.2407-0.0355-0.0540.2789-0.00330.2887-15.7206-6.1278-22.5201
41.20831.0580.64763.35840.51420.3293-0.03290.2062-0.30030.0020.0955-0.3505-0.18750.1394-0.01080.24420.030.04520.52050.0870.278-20.497312.3889-20.3919
52.5037-1.44561.34782.4935-0.77420.78610.0563-0.2191-0.0629-0.0571-0.0885-0.0120.1038-0.26640.04070.21770.06870.02840.36610.02780.1515-30.116-21.1275-8.5773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 302 )
4X-RAY DIFFRACTION4chain 'B' and (resid 10 through 145 )
5X-RAY DIFFRACTION5chain 'B' and (resid 146 through 302 )

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