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- PDB-5ep1: Quorum-Sensing Signal Integrator LuxO - Catalytic Domain -

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Basic information

Entry
Database: PDB / ID: 5ep1
TitleQuorum-Sensing Signal Integrator LuxO - Catalytic Domain
ComponentsPutative repressor protein luxO
KeywordsTRANSCRIPTION / Quorum sensing / AAA+ protein / catalytic 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 / Helicase, Ruva Protein; domain 3 - #60 ...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 / Helicase, Ruva Protein; domain 3 - #60 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative repressor protein luxO
Similarity search - Component
Biological speciesPhotobacterium angustum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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)28,4345
Polymers28,1981
Non-polymers2364
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.307, 76.307, 82.387
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: 28198.229 Da / Num. of mol.: 1 / Fragment: AAA+ catalytic domain (UNP residues 141-387)
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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris buffer pH8.0, 4 M ammonium acetate

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. obs: 43619 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 20.85 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.021 / Rrim(I) all: 0.061 / Χ2: 1.069 / Net I/av σ(I): 44.8 / Net I/σ(I): 8.6 / Num. measured all: 338644
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5370.33621620.9680.1310.3620.60699.4
1.53-1.557.50.30721620.9710.1180.330.581100
1.55-1.587.80.27221460.9760.1030.2920.608100
1.58-1.627.80.25221940.9830.0950.270.608100
1.62-1.657.70.21821900.9880.0830.2340.641100
1.65-1.697.40.19521660.9890.0760.210.654100
1.69-1.737.60.16721850.9930.0640.1790.678100
1.73-1.7880.14421420.9940.0530.1540.723100
1.78-1.8380.12921840.9940.0470.1370.764100
1.83-1.8980.10321780.9960.0380.110.84799.9
1.89-1.967.70.09321800.9970.0350.0990.94100
1.96-2.047.50.08421660.9970.0320.0891.033100
2.04-2.137.80.07321890.9970.0270.0781.12100
2.13-2.248.20.06621860.9980.0240.071.215100
2.24-2.3880.06321770.9980.0230.0671.3299.9
2.38-2.567.60.06121920.9970.0230.0651.481100
2.56-2.827.90.05721790.9980.0210.061.541100
2.82-3.238.20.05321950.9980.0190.0561.711100
3.23-4.077.60.0522000.9980.0190.0542.133100
4.07-357.90.04622460.9980.0170.051.98799.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10-2155_1692refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
RefinementResolution: 1.5→24.977 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1833 2188 5.03 %RANDOM
Rwork0.1622 41319 --
obs0.1632 43507 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.13 Å2 / Biso mean: 29.992 Å2 / Biso min: 15.51 Å2
Refinement stepCycle: final / Resolution: 1.5→24.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 16 221 2205
Biso mean--30.13 39.08 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012102
X-RAY DIFFRACTIONf_angle_d1.1452861
X-RAY DIFFRACTIONf_chiral_restr0.097319
X-RAY DIFFRACTIONf_plane_restr0.008381
X-RAY DIFFRACTIONf_dihedral_angle_d15.587805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4994-1.5320.25251560.21212513266999
1.532-1.56760.23831470.191525642711100
1.5676-1.60680.2231180.185526012719100
1.6068-1.65020.18511580.174225642722100
1.6502-1.69880.20681430.172525612704100
1.6988-1.75360.23641370.175125682705100
1.7536-1.81620.20321270.174225922719100
1.8162-1.88890.23371320.173625762708100
1.8889-1.97490.19111290.161425952724100
1.9749-2.07890.18211230.167225912714100
2.0789-2.20910.20451260.163425812707100
2.2091-2.37960.17031550.167425822737100
2.3796-2.61880.22571520.166125792731100
2.6188-2.99720.18321240.167726042728100
2.9972-3.77410.18261210.156926262747100
3.7741-24.98080.14241400.147726222762100

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