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- PDB-1h0m: Three-dimensional structure of the quorum sensing protein TraR bo... -

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Basic information

Entry
Database: PDB / ID: 1h0m
TitleThree-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA
Components
  • 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'
  • Transcriptional activator protein TraR
KeywordsTRANSCRIPTION/DNA / LUXR-TYPE PROTEIN / QUORUM SENSING / TRANSCRIPTIONAL REGULATOR / DNA-BINDING PROTEIN / HOMOSERINE LACTONE / TRAR / 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 speciesRhizobium radiobacter (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsVannini, A. / Volpari, C. / Gargioli, C. / Muraglia, E. / Cortese, R. / De Francesco, R. / Neddermann, P. / Di Marco, S.
Citation
Journal: Embo J. / Year: 2002
Title: The Crystal Structure of the Quorum Sensing Protein Trar Bound to its Autoinducer and Target DNA
Authors: Vannini, A. / Volpari, C. / Gargioli, C. / Muraglia, E. / Cortese, R. / De Francesco, R. / Neddermann, P. / Di Marco, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Transcriptional Regulator Trar Bound to its Cofactor and to a Specific DNA Sequence
Authors: Vannini, A. / Volpari, C. / Gargioli, C. / Muraglia, E. / De Francesco, R. / Neddermann, P. / Di Marco, S.
History
DepositionJun 25, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Dec 16, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_ref / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_gene_src_variant / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.details / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_site.pdbx_num_residues
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional activator protein TraR
B: Transcriptional activator protein TraR
C: Transcriptional activator protein TraR
D: Transcriptional activator protein TraR
E: 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'
F: 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'
G: 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'
H: 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,26812
Polymers130,3038
Non-polymers9654
Water1,51384
1
A: Transcriptional activator protein TraR
B: Transcriptional activator protein TraR
E: 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'
F: 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6346
Polymers65,1514
Non-polymers4832
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Transcriptional activator protein TraR
D: Transcriptional activator protein TraR
G: 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'
H: 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6346
Polymers65,1514
Non-polymers4832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.993, 94.678, 209.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0466, 0.9988, -0.0181), (-0.9987, 0.0469, 0.0181), (0.019, 0.0173, 0.9997)2.7998, 94.7708, 50.8009
2given(0.0886, 0.9956, -0.0317), (-0.9959, 0.0892, 0.0151), (0.0178, 0.0302, 0.9994)0.8146, 92.7003, 50.0746
DetailsTHE TETRAMERIC COMPLEX IS MADE UP BY TWO PROTEINCHAINS AND TWO DNA CHAINS. THERE ARE TWO SUCH TETRAMERSIN THE STRUCTURE AS INDICATED BY REMARK 350.

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Components

#1: Protein
Transcriptional activator protein TraR


Mass: 27060.037 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: TRANSCRIPTIONAL ACTIVATOR PROTEIN TRAR FROM AGROBACTERIUM TUMEFACIENS
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Description: ENCODED ON PLASMID PTIA6NC / Gene: traR / Variant: A348 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): B834-DE3 / References: UniProt: P33905
#2: DNA chain
5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3'


Mass: 5515.591 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: TRABOX / Source: (synth.) synthetic construct (others)
#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


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPOSITIVE REGULATOR OF CONJUGAL TRANSFER OF TI PLASMIDS. ACTIVATES TARGET GENES IN THE PRESENCE OF 3- ...POSITIVE REGULATOR OF CONJUGAL TRANSFER OF TI PLASMIDS. ACTIVATES TARGET GENES IN THE PRESENCE OF 3-OXYOCTANOYL-HOMOSERINE AND ALSO ACTIVATES TRAR AND TRAI.
Has protein modificationY

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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: 49.6 %
Crystal growpH: 6.2
Details: 50 MM MES PH 6.2, 200 MM CALCIUM ACETATE, 5% PEG 8000, 3 MM DTT.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.21 mMprotein1drop
250 mMMES1reservoirpH6.2
3200 mMcalcium acetate1reservoir
45 %(w/v)PEG80001reservoir
53 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979186, 0.979349
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791861
20.9793491
ReflectionResolution: 3→50 Å / Num. obs: 27075 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 10.3 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 21.8
Reflection shellResolution: 3→3.16 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 5.8 / % possible all: 98.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 278470
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
CNX2000.1refinement
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: MAXIMUM-LIKELIHOOD TARGET USING THE EXPERIMENTAL PHASE PROBABILITY DISTRIBUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1299 4.9 %RANDOM
Rwork0.233 ---
obs-26681 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.86 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 74.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.26 Å20 Å20 Å2
2--15.56 Å20 Å2
3----12.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7397 1464 68 84 9013
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 235 5.4 %
Rwork0.337 4099 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3AAI.PARWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMAAI.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.28 / 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_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

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