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- PDB-5l09: Crystal Structure of Quorum-Sensing Transcriptional Activator fro... -

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Entry
Database: PDB / ID: 5l09
TitleCrystal Structure of Quorum-Sensing Transcriptional Activator from Yersinia enterocolitica in complex with 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide
ComponentsQuorum-sensing transcriptional activator
KeywordsTRANSCRIPTION / alpha-beta structure / pheromone binding protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector ...Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-482 / ACETIC ACID / Quorum-sensing transcriptional activator
Similarity search - Component
Biological speciesYersinia enterocolitica serotype O:8 / biotype 1B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, Y. / Chhor, G. / Jedrzejczak, R. / Winans, S.C. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIAID-DMID-NIHA12011124 United States
CitationJournal: To Be Published
Title: Crystal Structure of Quorum-Sensing Transcriptional Activator from Yersinia enterocolitica
Authors: Kim, Y. / Chhor, G. / Jedrzejczak, R. / Winans, S.C. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Other / Structure summary
Category: citation_author / pdbx_SG_project ...citation_author / pdbx_SG_project / pdbx_audit_support / struct_keywords
Item: _citation_author.name / _pdbx_audit_support.funding_organization / _struct_keywords.text
Revision 1.4Oct 4, 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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Quorum-sensing transcriptional activator
B: Quorum-sensing transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,75619
Polymers42,3042
Non-polymers1,45117
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-44 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.878, 122.775, 107.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Quorum-sensing transcriptional activator


Mass: 21152.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081) (bacteria)
Strain: NCTC 13174 / 8081 / Gene: yenR, YE1599 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1JMX7

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Non-polymers , 5 types, 153 molecules

#2: Chemical ChemComp-482 / 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide


Mass: 213.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15NO4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 2.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29198 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 22.36 Å2 / Rsym value: 0.082 / Net I/σ(I): 23.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 5.34 / CC1/2: 0.935 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L07

5l07


Resolution: 2→31.939 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.77
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2774 5.1 %random
Rwork0.169 ---
obs0.1708 54350 97.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.3 Å2
Refinement stepCycle: LAST / Resolution: 2→31.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 93 136 2895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092858
X-RAY DIFFRACTIONf_angle_d0.9973851
X-RAY DIFFRACTIONf_dihedral_angle_d14.451723
X-RAY DIFFRACTIONf_chiral_restr0.055420
X-RAY DIFFRACTIONf_plane_restr0.005489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9937-2.02810.26611010.21172211X-RAY DIFFRACTION84
2.0281-2.06490.29871360.19782378X-RAY DIFFRACTION90
2.0649-2.10460.20821370.19762452X-RAY DIFFRACTION93
2.1046-2.14760.25181360.18682546X-RAY DIFFRACTION96
2.1476-2.19430.24111470.19432584X-RAY DIFFRACTION98
2.1943-2.24530.21741190.18762635X-RAY DIFFRACTION99
2.2453-2.30140.23971540.18482595X-RAY DIFFRACTION99
2.3014-2.36370.22551370.17572624X-RAY DIFFRACTION99
2.3637-2.43320.24441320.19252612X-RAY DIFFRACTION99
2.4332-2.51170.21981510.18532630X-RAY DIFFRACTION99
2.5117-2.60140.20181270.1792631X-RAY DIFFRACTION99
2.6014-2.70550.17871270.17142650X-RAY DIFFRACTION99
2.7055-2.82860.22671460.1662622X-RAY DIFFRACTION99
2.8286-2.97760.23781610.16692619X-RAY DIFFRACTION99
2.9776-3.1640.21241450.17042641X-RAY DIFFRACTION100
3.164-3.40810.17921480.16422613X-RAY DIFFRACTION100
3.4081-3.75060.19591560.15412633X-RAY DIFFRACTION100
3.7506-4.29220.17721620.14492639X-RAY DIFFRACTION100
4.2922-5.40340.1721460.14082642X-RAY DIFFRACTION100
5.4034-31.94310.17331060.1812619X-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)
10.00410.0028-0.00450.0105-0.00250.0043-0.0362-0.0243-0.0049-0.1044-0.0813-0.03290.01960.053400.13490.02420.0110.17670.01860.165219.7114.0482-9.3495
20.0305-0.00520.00110.0945-0.0060.07070.03210.08790.0897-0.0091-0.03680.0243-0.01970.034-0.0070.06240.00710.00130.09920.03520.131415.366925.9243-2.3972
30.00620.0054-0.00150.00870.00850.00590.0035-0.01080.00290.0630.03450.0296-0.0294-0.01690.0110.40550.03510.35580.3159-0.03070.23977.841616.05324.791
40.00830.0023-0.00110.00830.00130.0026-0.0291-0.04540.00710.1262-0.0007-0.00840.0231-0.0128-0.02580.6132-0.05770.11940.17840.0097-0.038417.57778.515126.2718
50.00190.0036-0.0030.0223-0.02950.036-0.00850.07120.00450.1697-0.026-0.0702-0.0090.0202-0.03350.1918-0.0059-0.03820.12570.00520.092923.59341.816715.1046
60.0008-0.0002-0.00130.0003-0.00040.00140.0170.0096-0.01810.02350.0167-0.00240.0021-0.0015-00.4581-0.04490.01260.19780.07550.152820.9354-5.705325.0618
70.013-0.00860.01420.007500.0185-0.06290.00760.00120.0874-0.0494-0.02360.00790.0328-0.01360.19490.00450.03560.12230.01510.112816.90689.213415.9015
80.00280.0012-0.00090.0014-0.0010.00040.01990.00180.01610.01540.00870.00890.0320.0036-00.2783-0.06090.04930.2190.03430.30615.0944-2.681712.7815
90.0071-0.00510.00470.0206-0.00680.01010.0191-0.03960.04610.08610.03650.0417-0.0947-0.00690.00060.19840.02010.18850.0906-0.02930.150510.827320.975317.4862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 165 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 27 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 61 )
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 105 )
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 129 through 144 )
9X-RAY DIFFRACTION9chain 'B' and (resid 145 through 169 )

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