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- PDB-5l07: Crystal Structure of Quorum-Sensing Transcriptional Activator fro... -

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Basic information

Entry
Database: PDB / ID: 5l07
TitleCrystal Structure of Quorum-Sensing Transcriptional Activator from Yersinia enterocolitica
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
ACETIC ACID / Quorum-sensing transcriptional activator
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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. / 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)43,36117
Polymers42,3042
Non-polymers1,05715
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-38 kcal/mol
Surface area16590 Å2
2
A: Quorum-sensing transcriptional activator
B: Quorum-sensing transcriptional activator
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)86,72234
Polymers84,6094
Non-polymers2,11430
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7500 Å2
ΔGint-109 kcal/mol
Surface area32730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.371, 123.399, 106.907
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 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 (bacteria) / Gene: yenR, ERS137951_02004 / Plasmid: pMCG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0T9SEJ2
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
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 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21587 / % possible obs: 97.3 % / Redundancy: 5.5 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.098 / Net I/σ(I): 17.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 3.07 / CC1/2: 0.824 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→34.661 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.65
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 1054 5.13 %random
Rwork0.1726 ---
obs0.1748 20559 92.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 64 75 2805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082796
X-RAY DIFFRACTIONf_angle_d0.8923767
X-RAY DIFFRACTIONf_dihedral_angle_d14.3851680
X-RAY DIFFRACTIONf_chiral_restr0.059408
X-RAY DIFFRACTIONf_plane_restr0.005479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1917-2.29150.27311040.20031930X-RAY DIFFRACTION75
2.2915-2.41220.22641230.18962327X-RAY DIFFRACTION89
2.4122-2.56330.25571220.19272434X-RAY DIFFRACTION93
2.5633-2.76120.23061230.18152471X-RAY DIFFRACTION95
2.7612-3.03890.2341400.1832576X-RAY DIFFRACTION98
3.0389-3.47830.24721560.17992561X-RAY DIFFRACTION98
3.4783-4.38090.18091450.15532576X-RAY DIFFRACTION97
4.3809-34.66520.18891410.16152630X-RAY DIFFRACTION95
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)
11.1292-0.0867-0.74260.6037-0.41912.20220.03140.44160.0216-1.0898-0.1154-0.5374-0.03030.327-0.34380.928-0.00230.72540.42980.07890.362425.135216.107129.016
20.74370.50620.46311.397-0.57631.6405-0.01210.2879-0.1086-1.76380.0961-0.07980.1708-0.13590.01630.8389-0.01320.01170.3051-0.05550.147512.4557.052831.3116
30.5118-0.25450.46490.1358-0.31253.46780.16370.4377-0.475-1.41630.2445-0.22030.6646-0.23380.57760.9306-0.05180.05470.2593-0.10060.42810.8084-4.66132.7449
41.24990.96260.39054.90461.76953.2143-0.02570.23-0.307-1.25140.0522-0.17530.28390.22010.1510.3295-0.01960.13950.17-0.00260.170417.1488.822937.9324
53.98891.65353.07612.94.16966.3205-0.2044-0.1689-0.68630.7062-0.05030.00551.17830.19410.12440.39840.07560.19750.34540.01920.621227.1158-1.481843.7027
63.333-0.33661.31475.42-2.75274.57380.01990.42820.4783-0.52480.168-0.2396-0.67730.3294-0.03250.4346-0.0090.23320.17790.06210.350621.212521.543735.7013
72.17260.6296-1.40395.00530.11864.4460.2264-0.2973-0.29930.5489-0.26180.3913-0.141-0.26450.12560.244-0.04020.04740.222-0.00780.182512.572414.93363.4057
89.1245-1.34691.79284.2084-0.35042.9190.0586-0.06320.13770.2208-0.31440.07880.28580.1040.15650.1597-0.02680.05390.2290.04920.197215.3123.291959.2794
93.0578-0.82920.61642.535-0.65542.151-0.0263-0.37870.42370.2671-0.07970.195-0.2943-0.37820.11940.150.03260.0020.2618-0.0830.31798.607430.742660.3878
101.4686-0.03650.45395.19872.62464.37570.05960.16840.5124-0.4027-0.0025-0.2075-0.2880.13270.08260.1515-0.0120.0460.17070.02320.229918.943329.822748.0259
111.9383-3.97430.46768.1837-0.93880.12350.0461-0.00690.4901-0.2260.1113-0.4084-0.75870.10530.04570.7645-0.2467-0.12490.75850.32440.927719.987339.155647.9092
127.7669-1.36265.28029.1344-3.50414.5029-0.16020.0931.44390.2029-0.0704-0.3784-0.75770.41540.10650.3735-0.0398-0.06640.5216-0.15110.62818.169339.004162.2212
134.30820.83180.1793.78220.95442.88280.1121-0.40880.09060.2847-0.07370.0016-0.0778-0.03840.01160.14910.00860.01420.15560.01190.157418.750424.964755.1488
144.870.60370.04922.74130.44462.695-0.09930.2211-0.3763-0.00020.1184-0.09960.122-0.11930.00790.1040.0281-0.02440.10690.03340.157316.705714.846155.4066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 109 )
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 133 )
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 144 )
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 170 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 27 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 38 )
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 68 )
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 85 )
11X-RAY DIFFRACTION11chain 'B' and (resid 86 through 96 )
12X-RAY DIFFRACTION12chain 'B' and (resid 97 through 105 )
13X-RAY DIFFRACTION13chain 'B' and (resid 106 through 133 )
14X-RAY DIFFRACTION14chain 'B' and (resid 134 through 170 )

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