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- PDB-2q0o: Crystal structure of an anti-activation complex in bacterial quor... -

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Basic information

Entry
Database: PDB / ID: 2q0o
TitleCrystal structure of an anti-activation complex in bacterial quorum sensing
Components
  • Probable transcriptional activator protein traR
  • Probable transcriptional repressor traM
KeywordsTRANSCRIPTION / helix-turn-helix / two-helix coiled coil
Function / homology
Function and homology information


: / quorum sensing / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional repressor TraM / Transcriptional repressor TraM superfamily / Prokaryotic Transcriptional repressor TraM / HR1 repeat / 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 profile. / Transcription regulator LuxR, C-terminal ...Transcriptional repressor TraM / Transcriptional repressor TraM superfamily / Prokaryotic Transcriptional repressor TraM / HR1 repeat / 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 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/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-LAE / Probable transcriptional activator protein TraR / Probable transcriptional repressor TraM
Similarity search - Component
Biological speciesRhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, G. / Jeffrey, P.D. / Fuqua, C. / Shi, Y. / Chen, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for antiactivation in bacterial quorum sensing.
Authors: Chen, G. / Jeffrey, P.D. / Fuqua, C. / Shi, Y. / Chen, L.
History
DepositionMay 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable transcriptional activator protein traR
B: Probable transcriptional activator protein traR
C: Probable transcriptional repressor traM
D: Probable transcriptional repressor traM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5626
Polymers77,0804
Non-polymers4832
Water8,719484
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.900, 62.480, 65.500
Angle α, β, γ (deg.)94.87, 110.45, 99.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Probable transcriptional activator protein traR


Mass: 26324.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium sp. (bacteria) / Strain: NGR234 / Gene: traR / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P55407
#2: Protein Probable transcriptional repressor traM


Mass: 12215.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium sp. (bacteria) / Strain: NGR234 / Gene: traM / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P55408
#3: Chemical ChemComp-LAE / 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE / N-(3-OXO-OCTANAL-1-YL)-HOMOSERINE LACTONE


Mass: 241.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 mM DTT, 60 mM HEPES, 120 mM CaCl2, 16.8% PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.127 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 9, 2005
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 55752 / Num. obs: 53940 / % possible obs: 96.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 1.96 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 5.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1.3 / Num. unique all: 5580 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L3L

1l3l


Resolution: 2→39.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1222632.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2694 5 %RANDOM
Rwork0.235 ---
obs0.235 53915 96.6 %-
all-55735 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.8909 Å2 / ksol: 0.336662 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--5.35 Å20.86 Å26.8 Å2
2---3.77 Å2-1.63 Å2
3---9.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 34 484 5568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 462 5.2 %
Rwork0.403 8393 -
obs-8393 95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3lae.paramlae.top

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