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- PDB-5ep0: Quorum-Sensing Signal Integrator LuxO - Receiver+Catalytic Domains -

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Basic information

Entry
Database: PDB / ID: 5ep0
TitleQuorum-Sensing Signal Integrator LuxO - Receiver+Catalytic Domains
ComponentsPutative repressor protein luxO
KeywordsTRANSCRIPTION / Quorum sensing / AAA+ protein / receiver domain / ATPase
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
: / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family ...: / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Putative repressor protein luxO
Similarity search - Component
Biological speciesPhotobacterium angustum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsShah, T. / Selcuk, H.B. / Jeffrey, P.D. / Hughson, F.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI054442 United States
CitationJournal: Plos Biol. / Year: 2016
Title: Structure, Regulation, and Inhibition of the Quorum-Sensing Signal Integrator LuxO.
Authors: Boyaci, H. / Shah, T. / Hurley, A. / Kokona, B. / Li, Z. / Ventocilla, C. / Jeffrey, P.D. / Semmelhack, M.F. / Fairman, R. / Bassler, B.L. / Hughson, F.M.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Putative repressor protein luxO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7279
Polymers44,0261
Non-polymers7018
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.149, 116.149, 71.174
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Putative repressor protein luxO


Mass: 44026.332 Da / Num. of mol.: 1 / Fragment: Receiver+catalytic domains (UNP residues 1-387)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium angustum (bacteria) / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1ZS18
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100 mM sodium buffer pH5.5, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9782 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2015
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. obs: 72082 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 21.29 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.018 / Rrim(I) all: 0.052 / Χ2: 0.906 / Net I/av σ(I): 39.619 / Net I/σ(I): 8.2 / Num. measured all: 563802
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.637.30.65135870.8830.2570.70.911100
1.63-1.667.50.55935790.9120.2180.6010.923100
1.66-1.697.50.51535790.9330.2010.5540.921100
1.69-1.727.90.42536030.9520.1610.4550.91100
1.72-1.7680.35435570.9640.1340.3790.94100
1.76-1.880.30636110.9730.1150.3270.956100
1.8-1.857.90.24935600.980.0940.2660.953100
1.85-1.97.80.236170.9870.0770.2140.963100
1.9-1.957.40.15735700.990.0620.1680.981100
1.95-2.027.70.13235880.9930.0510.1420.981100
2.02-2.097.90.10836130.9950.0410.1160.969100
2.09-2.178.20.08835970.9970.0330.0940.946100
2.17-2.278.10.07236340.9980.0270.0760.956100
2.27-2.397.90.06335880.9980.0240.0670.935100
2.39-2.547.60.05535970.9980.0210.0590.888100
2.54-2.747.90.04836080.9990.0180.0510.847100
2.74-3.018.30.04136190.9990.0150.0440.827100
3.01-3.457.90.03636070.9990.0140.0380.843100
3.45-4.347.80.0336540.9990.0110.0320.815100
4.34-357.90.02637140.9990.010.0280.68199.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10-2155_1692refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 1.6→23.091 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 3600 5 %RANDOM
Rwork0.1706 68421 --
obs0.1718 72021 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.6 Å2 / Biso mean: 29.475 Å2 / Biso min: 13.29 Å2
Refinement stepCycle: final / Resolution: 1.6→23.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 38 448 3439
Biso mean--35.56 42.21 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013169
X-RAY DIFFRACTIONf_angle_d1.0534321
X-RAY DIFFRACTIONf_chiral_restr0.068494
X-RAY DIFFRACTIONf_plane_restr0.007562
X-RAY DIFFRACTIONf_dihedral_angle_d12.2941984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5994-1.62040.30021350.24492560269597
1.6204-1.64260.25881330.221326312764100
1.6426-1.66610.22621310.218625932724100
1.6661-1.6910.23271560.204826082764100
1.691-1.71740.211410.205126122753100
1.7174-1.74550.19961440.193526342778100
1.7455-1.77560.21931370.199126172754100
1.7756-1.80790.22691340.191326422776100
1.8079-1.84260.20291500.189326042754100
1.8426-1.88020.22391410.182126362777100
1.8802-1.92110.19921200.185826272747100
1.9211-1.96580.21651350.183526252760100
1.9658-2.01490.20011460.178526122758100
2.0149-2.06930.221360.176926312767100
2.0693-2.13020.1841360.175726392775100
2.1302-2.19890.17081500.170826252775100
2.1989-2.27740.20971320.169426362768100
2.2774-2.36850.19051260.167726622788100
2.3685-2.47620.20271350.170626342769100
2.4762-2.60660.17871450.175426182763100
2.6066-2.76960.22381380.169126512789100
2.7696-2.98310.20391390.175426192758100
2.9831-3.28250.18531420.176726492791100
3.2825-3.75570.18441530.157126642817100
3.7557-4.72520.17041310.134926652796100
4.7252-23.09350.1931340.172627272861100

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