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- PDB-1l3l: Crystal structure of a bacterial quorum-sensing transcription fac... -

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Basic information

Entry
Database: PDB / ID: 1l3l
TitleCrystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA
Components
  • 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'
  • Transcriptional activator protein traRActivator (genetics)
KeywordsTRANSCRIPTION/DNA / helix-turn-helix DNA binding motif / alpha/beta/alpha sandwich / asymmetry of the protein-DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


quorum sensing / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region 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 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 ...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 / 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 / DNA / DNA (> 10) / Transcriptional activator protein TraR
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 Å
AuthorsZhang, R. / Pappas, T. / Brace, J.L. / Miller, P.C. / Oulmassov, T. / Molyneaux, J.M. / Anderson, J.C. / Bashkin, J.K. / Winans, S.C. / Joachimiak, A.
CitationJournal: Nature / Year: 2002
Title: Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA.
Authors: Zhang, R.G. / Pappas, T. / Brace, J.L. / Miller, P.C. / Oulmassov, T. / Molyneaux, J.M. / Anderson, J.C. / Bashkin, J.K. / Winans, S.C. / Joachimiak, A.
History
DepositionFeb 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'
F: 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'
G: 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'
H: 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'
A: Transcriptional activator protein traR
B: Transcriptional activator protein traR
C: Transcriptional activator protein traR
D: Transcriptional activator protein traR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,74112
Polymers132,7768
Non-polymers9654
Water16,466914
1
E: 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'
G: 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'
B: Transcriptional activator protein traR
D: Transcriptional activator protein traR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8716
Polymers66,3884
Non-polymers4832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'
H: 5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'
A: Transcriptional activator protein traR
C: Transcriptional activator protein traR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8716
Polymers66,3884
Non-polymers4832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.298, 58.370, 127.453
Angle α, β, γ (deg.)90.00, 102.81, 90.00
Int Tables number4
Space group name H-MP1211
Detailsdeposited coords. are two protein-DNA-pheromone complexes in asymmetric unit

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Components

#1: DNA chain
5'-D(*GP*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP*CP*TP*GP*CP*AP*CP*AP*TP*C)-3'


Mass: 6133.978 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
Transcriptional activator protein traR / Activator (genetics) / Quorum-Sensing Transcription Factor


Mass: 27060.037 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Plasmid: pJZ358 / Production host: Escherichia coli (E. coli) / Strain (production host): B21(DE3) / References: UniProt: P33905
#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.: 4 / Source method: obtained synthetically / Formula: C12H19NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 914 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Joachimiak, A., (1991) Methods Enzymol., 208, 82.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9797, 0.95600
DetectorType: SBC-2 / Detector: CCD / Date: Aug 12, 2000 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.9561
ReflectionResolution: 1.66→50 Å / Num. all: 155406 / Num. obs: 139194 / % possible obs: 89.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.69 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.76
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 5.29 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2 / Num. unique all: 10916 / % possible all: 70.9
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
Rmerge(I) obs: 0.422

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Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.66→39.6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 845189.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 7044 5.1 %RANDOM
Rwork0.246 ---
all-139194 --
obs-139194 89.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.7694 Å2 / ksol: 0.337305 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å21.12 Å2
2---2 Å20 Å2
3---3.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.66→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7332 1628 68 914 9942
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it0.841.5
X-RAY DIFFRACTIONc_mcangle_it1.282
X-RAY DIFFRACTIONc_scbond_it1.532
X-RAY DIFFRACTIONc_scangle_it2.222.5
LS refinement shellResolution: 1.66→1.76 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 907 4.9 %
Rwork0.336 17485 -
obs--70.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPHERMONE_SNEW.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION4PHERMONE_SNEW.PARWATER.TOP
Refinement
*PLUS
Rfactor Rfree: 0.252 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor Rfree: 0.341 / Rfactor Rwork: 0.336

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